Lep-MAP3 Activity
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Activity for Lep-MAP3
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Afewerki Yohannes Kiros posted a comment on discussion General Discussion
Dear Pasi, Thank you so much for your response and valuable suggestion. Regards, Afewerki
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Pasi Rastas posted a comment on discussion General Discussion
Dear both, I think you can analyse such data as F2 by setting P1-P4 to grandparents, adding dummy parents and then F7 as offspring. Cheers, Pasi
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Nicolas posted a comment on discussion General Discussion
Dear Pasi, No worries at all on the delay - I really appreciate you taking the time to respond over the summer and thank you for updating the wiki. Hope you had a great holiday. I will give this a go later this week. Fingers crossed it all works smoothly! Best, Nick
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Dear Pasi, I have also similar question as @chenli. Would you please give us a direction to proceed with the linkage mapping analysis? Thank you so much for your kind support. Sincerely, Afewerki
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Dear Nick, There should be documentation in the wiki now about linkage mapping without parents. Please ask if it is not clear. However, it might be possible that your data can be analysed without any of these tricks. Just analyse the data as known parents, the sex averaged map will work anyway... Cheers, Pasi
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There should be documentation in the wiki now. Please ask if it is not clear. Cheers, Pasi
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LM3 Home
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Dear Farid, Sorry, I don't know any software to do this. For best results, I would run SeparateChromosomes2 on all markers, and only then would do the thinning of markers in the linkage groups so that the markers selected will be contributing to the map. Probably good result would be obtained by thinning markers after ParentCall2 or Filtering2 on all markers. Cheers, Pasi
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Faridul Islam posted a comment on discussion General Discussion
Dear Pasi, Thanks for your reply. I was waiting for your suggestions. Your reply clarified most of my confusion except the last issue regarding thinning sequencing data. Could you suggest any tool by which I can make specific window bin size and select one makers from that window bin or I need to create my own bash script for that purpose? Your suggestion would be highly appreciated. Best Regards, Farid
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LM3 Home
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Dear Farid, For the first question, I think it due to fact that Filtering2 will remove some distorted markers (dataTolerance=0.001) and after this, some of them might become non-informative. So ParentCall2 will do this filtering without taking into account the distortion. Typically I don't include removeNonInformative in Filtering2 as then I can easily use datasets with different dataTolerance values, if needed, as the number of markers stays the same. The second one: Yes, you can use your genome...
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LM3 Home
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LM3 Home
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Dear Nick, Thank you for your question and sorry for taking some time to answer as I was on holiday. I think you can construct the map as if there were no parental data. This has been in the discussion earlier. I will add the information to the wiki soon. If you are in a hurry, please check the wiki and the old discussion threads. Cheers, Pasi
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LM3 Home
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Dear Pasi, Today I got a couple of issues to discuss, and I could also use some advice on another issues. First of all, I ran into a weird thing with the "removeNonInformative" argument. Since it works in both ParentCall2 and Filtering2 modules, I tried it out in two ways: 1. Option-1: I used "removeNonInformative" argument in ParentCall2 module, then Filtering2 module with dataTolerance=0.001 argument . 2. Option-2: I used both "removeNonInformative" and dataTolerance=0.001 argument in Filtering2...
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Dear Pasi, Thanks for developing Lep-MAP and Lep-Anchor. We've had great success using it for linkage mapping in corals and recently submitted a manuscript for a linkage map comparison. In the maps where we've had success, the species were hermaphrodites but crosses were performed such that we knew which parent was the egg donor and which was the sperm donor. We are now moving on to a set of crosses where we don't have this information. In these crosses, sperm and eggs from each parent were all mixed...
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Dear Pasi, Thanks for developing Lep-MAP and Lep-Anchor. We've had great success using it for linkage mapping in corals and recently submitted a manuscript for a linkage map comparison. In the maps where we've had success, the species were hermaphrodites but crosses were performed such that we knew which parent was the egg donor and which was the sperm donor. We are now moving on to a set of crosses where we don't have this information. In these crosses, sperm and eggs from each parent were all mixed...
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Dear Pasi, Thanks for developing Lep-MAP and Lep-Anchor. We've had great success using it for linkage mapping in corals and recently submitted a manuscript for a linkage map comparison. In the maps where we've had success, the species were hermaphrodites but crosses were performed such that we knew which parent was the egg donor and which was the sperm donor. We are now moving on to a set of crosses where we don't have this information. In these crosses, sperm and eggs from each parent were all mixed...
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Dear Jess, This is very odd indeed. Note that the map position of a marker can be impossible to determine exactly. You can output the map position intervals from OrderMarkers2 (calculateIntervals=file) to see the uncertainty in the map positions. You can also try parameter usePhysical (you can tinker it to find a suitable value) to have a map between the physical order and "de novo". Cheers, Pasi
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Yess Alvarez modified a comment on discussion General Discussion
Dear Pasi, Thank you for clarifying my doubts! I have run OrderMarkers2 with improveOrder=1 to observe potential structural variations in CHR16. However, when I run the Marey map, the positions of the markers are dispersed. I'm confused about what this means. I share the command and the charts. > java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= ./order_CHR_phys/order_CHR16.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=1 > eval_order/eval_CHR16_run1.2.txt...
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Dear Pasi, Thank you for clarifying my doubts! I have run OrderMarkers2 with improveOrder=1 to observe potential structural variations in CHR16. However, when I run the Marey map, the positions of the markers are dispersed. I'm confused about what this means. I share the command and the charts. > java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= ./order_CHR_phys/order_CHR16.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=1 > eval_order/eval_CHR16_run1.2.txt...
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Dear Pasi, Thank you for clarifying my doubts! I have run OrderMarkers2 with improveOrder=1 to observe potential structural variations in CHR16. However, when I run the Marey map, the positions of the markers are dispersed. I'm confused about what this means. I share the command and the charts. > java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= ./order_CHR_phys/order_CHR16.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=1 > eval_order/eval_CHR16_run1.2.txt...
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Dear Jess, Nice to hear from your progress! The red lines in the first LMPlot are indicating a loop in the graph. It means that there is a recurring crossover in this region. It could be an inversion between the reference order and the map order. As there is only one recurring crossover, this is not a big deal, it only adds two extra crossovers (at most, as this could be correct solution as well). The second one is harder to figure out (if you run LMPlot again, it will untangle the graph in a different...
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Dear Jess, Nice to hear from your progress! The red lines in the first LMPlot are indicating a loop in the graph. It means that there is a recurring crossover in this region. It could be an inversion between the reference order and the map order. As there is only one recurring crossover, this is not a big deal, it only adds two extra crossovers (at most, as this could be correct solution as well). The second one is harder to figure out (if you run LMPlot again, it will untangle the graph in a different...
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Dear Pasi, I've managed to obtain 24 LGs as expected according to the reference genome (24 chromosomes). This is the command I used: java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= order_CH1.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=0 calculateIntervals=intervals_markers_CH1.txt > eval_CHR1.txt But I have some questions regarding the results: I have created LMPlots for each one to observe the order of the markers, and I noticed that...
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Dear Pasi, I've managed to obtain 24 LGs as expected according to the reference genome (24 chromosomes). This is the command I used: java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= order_CH1.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=0 calculateIntervals=intervals_markers_CH1.txt > eval_CHR1.txt But I have some questions regarding the results: I have created LMPlots for each one to observe the order of the markers, and I noticed that...
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Dear Pasi, I've managed to obtain 24 LGs as expected according to the reference genome (24 chromosomes). This is the command I used: java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= order_CH1.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=0 calculateIntervals=intervals_markers_CH1.txt > eval_CHR1.txt But I have some questions regarding the results: I have created LMPlots for each one to observe the order of the markers, and I noticed that...
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Dear Pasi, I've managed to obtain 24 LGs as expected according to the reference genome (24 chromosomes). This is the command I used: java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= order_CH1.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=0 calculateIntervals=intervals_markers_CH1.txt > eval_CHR1.txt But I have some questions regarding the results: I have created LMPlots for each one to observe the order of the markers, and I noticed that...
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Dear Pasi, Thanks for the info! I'll let you know if I run into any problems. Seriously, this tool you built is awesome! It makes dealing with giant mapping datasets so much easier. Hope Jesi was able to fix the issue! Good luck to Jesi too. Best regards, Farid
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Dear Jesi, You can merge and split linkage groups in the process as you like: #merge lgs 1 & 2 awk '(($4==1 || $4==2) && $2=="CHR1")' numeric_snsp.txt >order1.phys #split lg 3 awk '($4==3 && $2=="CHR3")' numeric_snsp.txt >order3.phys awk '($4==3 && $2=="CHR4")' numeric_snsp.txt >order4.phys Maybe it is best to figure out how the LGs and chrs correspond to each other and why they are not corresponding 1 to 1. Cheers, Pasi
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Dear Pasi, Thanks a lot for your help! I followed your advice and managed to get the files. However, while analyzing numeric_snps.txt, I found that my LG1 doesn't correspond to chromosome 1. In fact, it contains markers for chromosome 5 (165 markers) and chromosome 18 (151 markers). I think, I could try running SeparateChromosome2 for this LG and observe if they separate. Is this possible? If so, how should I proceed? On the other hand, I found two linkage groups (LG21= 60 markers and LG24=53 markers)...
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Dear Jesi, The example is indeed for creating both, the de novo map and the physical map. The order1.input is the denovo map for Lep-Anchor. However, you need the linkage groups only for the physical order (you can try to put all markers in a chromosomal assembly but this might cause problems as there are very likely some "jumping" markers). If you have the snp names (snps.txt) and linkage groups from SeparateChromosomes2 (map_lg.txt) you can try something like this: paste snps.txt map_lg.txt|awk...
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Dear Jesi, The example is indeed for creating both, the de novo map and the physical map. The order1.input is the denovo map for Lep-Anchor. However, you need the linkage groups only for the physical order (you can try to put all markers in a chromosomal assembly but this might cause problems as there are very likely some "jumping" markers). If you have the snp names (snps.txt) and linkage groups from SeparateChromosomes2 (map_lg.txt) you can try something like this: paste snps.txt map_lg.txt|awk...
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Dear Jesi, The example is indeed for creating both, the de novo map and the physical map. The order1.input is the denovo map for Lep-Anchor. However, you need the linkage groups only for the physical order (you can try to put all markers in a chromosomal assembly but this might cause problems as there are very likely some "jumping" markers). If you have the snp names (snps.txt) and linkage groups from SeparateChromosomes2 (map_lg.txt) you can try something like this: paste snps.txt map_lg.txt|awk...
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Dear Jesi, The example is indeed for creating both, the de novo map and the physical map. The order1.input is the denovo map for Lep-Anchor. However, you need the linkage groups only for the physical order (you can try to put all markers in a chromosomal assembly but this might cause problems as there are very likely some "jumping" markers). If you have the snp names (snps.txt) and linkage groups from SeparateChromosomes2 (map_lg.txt) you can try something like this: paste snps.txt map_lg.txt|awk...
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Hi pasi and Farid, I´m in a similar situation. I have used a reference genome from a very closely related species to my species of interest for SNP calling. Since I know the physical position of the markers, I want to create a linkage map based on this known order. Reading the wiki on how to generate this file, I found: awk -f liftover chr1.agp order1.input|sort -V|grep CHR >order1.liftover - assuming scaffolds/contigs are named CHR.... (default for makeagp*) awk -vinverse=1 -f liftover chr1.agp...
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Dear Farid, Thank you for your question. The parameter combo evaluateOrder and improveOrder=0 is the way. The order must be given with the numerical identifiers. Lep-Anchor wiki contains some examples of this: http://sourceforge.net/projects/lep-anchor . Cheers, Pasi
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Dear Pasi, We previously addressed an issue with the Filtering2 command in another thread. Today, I'd like to discuss a different topic related to linkage map generation. I have access to the reference genome for the plant I'm studying, which was used for SNP calling. Since I know the physical position of the markers, I want to create a linkage map based on this known order. On the Wiki page, I found the following command: java -cp bin/ OrderMarkers2 evaluateOrder=order2.txt data=data_f.call improveOrder=0...
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Dear Dave, Thank you for your question. Typically you end up with many small groups and hopefully desired number of large groups. If you end up collapsing two or more groups, you can re-run SeparateChromosomes2 again with the map parameter giving the previous result (and a higher lodLimit). The collapsed group is most likely the largest (lg=1), but if it is not the parameter lg can be given. The small groups can be removed manually or with the parameter sizeLimit. Cheers, Pasi
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Dear Dave, Thank you for your question. Typically you end up with many small groups and hopefully desired number of large groups. If you end up collapsing two or more groups, you can re-run SeparateChromosomes2 again with the map parameter giving the previous result (and a lower lodLimit). The collapsed group is most likely the largest (lg=1), but if it is not the parameter lg can be given. The small groups can be removed manually or with the parameter sizeLimit. Cheers, Pasi
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Dear Dave, Thank you for your question. Typically you end up with many small groups and hopefully desired number of large groups. If you end up collapsing two or more groups, you can re-run SeparateChromosomes2 again with the map parameter giving the previous result. The collapsed groups is most likely the largest (lg=1), but if it is not the parameter lg can be given. The small groups can be removed manually or with the parameter sizeLimit. Cheers, Pasi
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Dear Lorenzo, I think your version of LM3 is recent enough. The problem you are having is probably due to not using the same phasing for LOD computation and map evaluation. Safer option is to calculate LOD scores for each 10 runs and pick the LOD result based on the likelihoods (instead of evaluateOrder). You could also use the map from evaluateOrder output. The parameter phasingIterations=3 might improve the evaluated order's phasing... Cheers, Pasi
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Lorenzo Bertola posted a comment on discussion General Discussion
Hello Pasi! Thank you for the follow up. We are using the version from December 2023. Should we try a newer version? The names in the LOD output match the names and position of markers in the map file. We first ran orderMarkers for each LG 10 times and selected the order with the best likelihood, and then re-ran orderMarkers with the best order to produce the LOD file with the below command. java -cp lepmap/bin/ OrderMarkers2 \ data=2_filtered_LepMap_fam3 \ evaluateOrder=6_LepMap_fam3_${LG} \ improveOrder=0...
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Hello Pasi! Thank you for the follow up. We are using the version from December 2023. Should we try a newer version? The names in the LOD output match the names and position of markers in the map file. We first ran orderMarkers for each LG 10 times and selected the order with the best likelihood, and then re-ran orderMarkers with the best order to produce the LOD file with the below command. java -cp lepmap/bin/ OrderMarkers2 \ data=2_filtered_LepMap_fam3 \ evaluateOrder=6_LepMap_fam3_${LG} \ improveOrder=0...
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Dave posted a comment on discussion General Discussion
Hello Pasi, I am currently learning to use Lepmap3 and have encountered some issues that I would like to consult with you. After performing SeparateChromosomes2, is it necessary for the number of obtained LGs to exactly match the number of chromosomes in the species and correspond one-to-one? Despite trying numerous LOD , I have not obtained the desired results. If the number of LGs obtained exceeds the number of chromosomes, can I remove the extra LGs and keep only the appropriate LGs for OrderMarkers2?...
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Dear Lorenzo, Thank you for your question. I did not find any obvious problem with the code for calculating unique map positions (this routine is only used in the LOD calculation). I even tried in on real data, I got 147 unique positions from the LOD and from the map. Are you using the latest version of LM3? Some older versions used identicalLimit parameter in finding these unique positions. The LOD output contains the marker names, did you check the positions for these markers from the map? Cheers,...
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Dear Lorenzo, Thank you for your question. I did not find any obvious problem with the code for calculating unique map positions (this routine is only used in the LOD calculation). I even tried in on real data, I got 147 unique positions is LOD and from the map. Are you using the latest version of LM3? Some older versions used identicalLimit parameter in finding these unique positions. The LOD output contains the marker names, did you check the positions for these markers from the map? Cheers, P...
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Hello Pasi, I am trying to do some testing using the LOD output matrix from the orderMarkers module, but I am struggling to understand what the positions in the columns represent. For a single linkage group I mapped 793 markers across 3 families. The resulting maps have: - female map: 101 unique positions - male map: 61 unique positions - sex-averaged map*: 157 unique positions. The LOD file has the correct number of rows (793), one row per mapped marker, but it only has 148 columns, thus 147 unique...
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Dear Farid, Thanks for noting this. I will try to test the software in windows as well. This might also help: you can (maybe) add -Dline.separator=$'\n' to java command to set the end of line separator to \n. Or to -Dline.separator=$'\r\n' if it then works. Cheers, Pasi
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Dear Yess Alvarez, Normally you just construct one map, it will have male and female position for each marker. You can construct separate male and female maps as well, but you should first try with all markers. Cheers, Pasi
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Dear Pasi, Thank you for sharing your knowledge. I'm just starting to use Lepmap3. My goal is to create a genetic map from an F1 (fullsib population). I have some doubts about how to do it. I already have my VCF file, but not the pedigree. I understand that I should create separate maps for each parent (mother and father), and then combine them with the offspring's map. How can I do this with LepMap3? Sorry if my question is very basic, I'm a beginner! Thank you very much!
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Dear Pasi, Thank you for sharing your knowledge. I'm just starting to use Lepmap3. My goal is to create a genetic map from an F1 (fullsib population). I have some doubts about how to do it. I already have my VCF file, but not the pedigree. I understand that I should create separate maps for each parent (mother and father), and then combine them with the offspring's map. How can I do this with LepMap3? Sorry if my question is very basic, I'm a beginner! Thank you very much!
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Dear Pasi, Thanks for your reply! You were right about the end-of-line issue. I ran the same command and data in the Linux environment within Windows (WSL2), and it worked successfully. Out of curiosity, like I mentioned earlier, ParentCall2 was able to read my data and generate a "CALL File." However, Filtering2 couldn't read this same "CALL File." This makes it seem like ParentCall2 might not be creating a correct "CALL File." Interestingly, in the Linux system, Filtering2 had no problem reading...
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Dear Farid, Thank you for your question and sorry to hear you about your problem with Lep-MAP3. I cannot find anything wrong in your commands, they seem ok. The error message is originating from the part where the data is read and the marker name is extracted. Lep-MAP3 does not find two tab separated fields from the line. I cannot say exactly what the problem is. Maybe it is the end of line characters (\r\n) in dos? I know that some windows text editors can fix/change these (I haven't used windows...
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Dear Farid, Thank you for your question and sorry to hear you about your problem with Lep-MAP3. I cannot find anything wrong in your commands, they seem ok. The error message is originating from the part where the data is read and the marker name is extracted. Lep-MAP3 does not find two tab separated fields from the line. I cannot say exactly what the problem is. Maybe it is the end of line characters (\r\n) in dos? I know that some windows text editors can fix/change these. (I haven't used windows...
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Dear Pasi, I just started using Lep-MAP3 (v. 0.5) for linkage map construction for F2 self-crossed tomato population. ParentCall2 successfully read my data and saved the data for next stage. I did not use the "removeNonInformative=1" options when running ParentCall2. Here is the ParentCall2command I used: java -cp .\bin\ ParentCall2 data=tomato_F2_pedigree.txt vcfFile=format_2_final_for_mapping.vcf >t_data_p.call However, I encountered Error:504 when running Filtering2 with "dataTolerance=NUM" and...
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Dear Tianzhu, The parameter minError controls how much you trust your data. It will cap the genotype quality to this value, 0.1 is phred score of 10. If this is RADseq data, very useful parameter is proximityScale, value of 50 or 100 might work for most data to scale down the effect of too close by SNPs (from the same RAD site). I would be more interest on how you generated the input genotype data. Maybe the problem is there? Cheers, Pasi
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Tianzhu Xiong posted a comment on discussion General Discussion
Hi Pasi, Thanks for your help in previous posts. I have gone back to do more research on this dataset. As you said 200-300 markers per chromosome are indeed still small. This cross involves ~180 progenies from 6 families of crosses (just parent-offpsring, no grandparents). A previous researcher working on this call data used the following command for OrderMarkers2, let's say it's Version A: java OrderMarkers2 map=map.txt data=- numThreads=2 recombination2=0 chromosome=1 informativeMask=1 minError=0.1...
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Dear Yutang, Yes, it is consistent. Cheers, Pasi
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Yutang Chen posted a comment on discussion General Discussion
Dear Pasi, I hope you are well. It seems my last reply to your last respond didn't get posted. So here I write to you again. Yes, you are absolutely right. To determine the phase among linkage groups in one parent, data of grandparents are needed. Actually, my question should be whether the first haplotype in the phased parental genotypes is consistently grandmother or grandfather haplotype among linkage groups. Thank you very much for your help, and please have a nice week. Best wishes, Yutang
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Dear Yutang, In the phase information, first there is the paternal phased genotype (e.g. GA) and then, separated by "," is the maternal one (each family separated by ";"). The two haplotypes are in arbitrary order (but you know that they are the fathers two haplotypes and the mothers two haplotypes). If you use grandparents for phasing, then the first is inherited from the parent's father and second from the parent's mother. Cheers, Pasi
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Dear Yutang, In the phase information, first there is the paternal phased genotype (e.g. GA) and then, separated by "," is the maternal one (each family separated by ";"). The two haplotypes are in arbitrary order (but you know that they are the fathers two haplotypes and the mothers two haplotypes). If you use grandparents for phasing, then the first is the parent's father's and second the parent's mother's. Cheers, Pasi
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Dear Yutang, In the phase information, first there is the paternal genotype (e.g. GA) and then, separated by "," is the maternal one (each family separated by ";"). The two haplotypes are in arbitrary order (but you know that they are the fathers two haplotypes and the mothers two haplotypes). If you use grandparents for phasing, then the first is the parent's father's and second the parent's mother's. Cheers, Pasi
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Dear Pasi, I have another question: is the first haplotype consistently the mother or father haplotype among linkage groups? Thank you very much. Best wishes, Yutang
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Dear Pasi, Just want to let you know, with the Lep-MAP3 variant calling pipeline, I successfully got the parental phase! By the way, just want ask, would the phase change if I order the markers based on the given order? Or, the other way around, I used the given order (order from base pair position) to order the markers, if I don't use a given order, would the phase be different? Thank you very much. Best wishes, Yutang
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Never mind, Pasi, I am running your variant calling pipeline now. I will get back to you when I get the results. Best wishes, Yutang
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Dear Pasi, I think I need your help now. I have the vcf file generated by bcftools as input, and the parental genotypes I got from OrderMarkers2 are all AC or CA. I guess this is because as you said you just convert 0,1,2,3 to A,C,G,T, respectively, even though 0 or 1 might not really correspond to A or C. So, if I want to get genotypes with the correct ACGT codes, then I have to follow the Lep-MAP3 variant calling pipeline. Is this right? Can I convert vcf file to the genotype likelihoods? Thank...
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Dear Pasi, Very happy to hear from you! Two days ago, I was just too excited thinking that it might be a good idea to add a separator. Now, after reading more carefully of the new features, I realized that there is no need to add a separator between alleles. Just now, I was about to write to tell you to ignore what I said, but I found you already replied. Very sorry and always appreciate your quick response and support! I will try the new scripts first and update you what I find. Again, great job!...
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Dear Yutang, Nice to hear from you. And thanks for the suggestion, the phase information has been very useful. I added it soon after the PAG meeting where we discussed it. I have used the phase for so many projects, that I would not want to change the format anymore. There is the vcfPhase.awk script (in scripts.zip) that adds "|" between alleles for vcf input (AT=>0|1). This could be modified to change AT=>A|T. Note that the ACGT codes are correct only for the Lep-MAP3 variant calling. For vcf input,...
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Dear Pasi, I hope you are well. It has been more than one year since we last met at PAG where we shortly discussed generating parental phase. I was just reading the Summary page of Lep-MAP3 and I found in the second picture of Project Samples, you actually added a column of parental phase in the output file of ordermarkers2! This is so great! Thank you very much. One thing I would like to confirm is, for example, in the mother phased genotype, is it true that alleles at the left or right side belong...
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Recoquillay Julien posted a comment on discussion General Discussion
Thanks Pasi. I did not see that you had answered. So basically, JoinSingle2All said this : If you asked for the high and technically allowing anything LOD of 30, SNP goes to Linkage Group 34. If asked for a lower LO of 4.4 -> LG 3 and a lower again LOD of 3.3 -> LG 4 Many thanks, I understand better the output now.
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Dear Tianzhu, I think this is about the quality of your data and number of markers. I would aim for a higher number of markers, often you get about 1000 markers per chr with RADseq and 200 markers is still quite few. Moreover, I have no idea how you have analysed and processed your data, these are critical steps in the map construction. Cheers, Pasi
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Hi Pasi, Thanks for the quick response. 75cM is fine in my view too, but only when the extra 25cM is produced by, for instance, double crossovers, which would still keep the recombination probability capped at 0.5. It seems to happen to almost all (longer) chromosomes in the data so I was a bit suspicious what could be going on. It's extremely interesing that you mentioned chromatid interference: If two COs are favored between nonoverlapping sets of chromatids then it would push recombination probability...
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Dear Tianzhu, Aha. We are talking about different thing here. I thought there was 0.7 fraction of crossovers between two adjacent markers (rf in the mapping functions). The map is about 75 cM. It is within my expected range of 50-80 cM. If you think this is too long, check if there are individuals that recombine too many times over all chrs. I think you can get this information from the Lep-MAP3's error stream output. You can also force Lep-MAP3 to produce shorter maps by changing the scale parameter....
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Dear Tianzhu, Aha. We are talking about different thing here. I thought there was 0.7 fraction of crossovers between two adjacent markers (rf in the mapping functions). This makes sense. The map is about 75 cM. It is within my expected range of 50-80 cM. If you think this is too long, check if there are individuals that recombine too many times over all chrs. I think you can get this information from the Lep-MAP3's error stream output. You can also force Lep-MAP3 to produce shorter maps by changing...
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Hi Pasi, For instance, in the attached map for chromosome 2, I plotted paternal haplotypes on the left-hand side (black-white corresponds to 0-1 in inferred phase -- the phase is NOT the grandparental phase and grandparents were not used for linkage analysis). On the right-hand side, I plotted three quantities: the p-curve (blue): the probability of recombination for a given marker with the left-most marker the q-curve (yellow): the probability of recombination for a given marker with the right-most...
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Hi Pasi, For instance, in the attached map for chromosome 2, I plotted paternal haplotypes on the left-hand side (black-white corresponds to 0-1 in inferred phase). On the right-hand side, I plotted three quantities: the p-curve (blue): the probability of recombination for a given marker with the left-most marker the q-curve (yellow): the probability of recombination for a given marker with the right-most marker the Marey map (red): the cumulative mapping distance The probability of recombination...
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Dear Tianzhu, Could you post the map ends from Lep-MAP3, and maybe the commands you have used? I have not seen over 0.5 recombination fractions. Are you using grandparents for phasing? Without grandparents, I think the Lep-MAP3 phasing algorithm should flip 0.7 in this case to 0.3. Proximityscale should be about the length of the RAD site. Value of 100 (in bp) should be ok for most cases. Cheers, Pasi
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Hi Pasi, Thanks for the insight about this problem. Recombination probability in meiosis is capped at 0.5 between any pair of markers (i.e., markers separated by an even number of recombination breakpoints = no recombination between markers), so that's why I think a recombination probability of 0.7 is abnormally high. I will check the IBD values between offspring and between parent-offpspring. Is the new flag proximityScale added only recently? May I ask what is the general guidance for setting its...
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Dear TZ, Thank you for your question. My maps for Lepidoptera has been 50-80cM. If there are poor markers, these tend to go to the map ends. Maybe this is the case here. Removing markers from the ends might solve the problem. The new default mapping function is Morgan, so recombination rate of 0.7 produces 70cM gaps. For other mapping functions, this would break the linkage group. Also check that the data correct, for example IBD values between parents and offspring are about 0.5 or higher. If your...
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Dear Pasi, I am recently pondering over some linkage maps produced from an F2 cross including just parents and offspring in Lepidoptera. Markers are from RADseq, about 130-200 markers per chromosome with about 175 offspring. I used markers informative to only the paternal parent to infer male-recombination, and some chromosomes have maps much longer than 50cM. However, upon inspecting haplotypes, the recombination probability between markers towards each end of the chromosome is much higher than...
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chinj cheung posted a comment on discussion General Discussion
Dear pasi, Thank you for your reply. thanks, Chinj Cheung
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Dear chinj cheung, Lep-MAP3 requires data with both parental genotypes. ParentCall2 tries to impute missing parents if it is possible. This imputation is difficult if you have only few offspring and no grandparents or half-sib families. Family limit defines how certain the imputed parental genotypes must be. Lowering it might yield more data but there might be more errors as well. I have constructed good maps with ignoreParentOrder as well. This might help more if both parents are missing as it keeps...
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Dear pasi, Yes! I have approximately 1200 single-parent families and around 200 two-parent families. To clarify, when running ParentCall2, should I add the parameters familyLimit=1(1.5) and ignoreParentOrder=1, where ignoreParentOrder means that the order of the parents' genotypes need not be taken into account? But this statement "makes the map construction more difficult (it requires extra parameters in other modules as well)" implies that I should pay attention to what during the subsequent map...
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Dear chinj cheung, Wow, this is a huge dataset! If you have a lot of small families with only one parent, it might happen that the parental genotypes cannot be inferred. In this case you also obtain all 1s. You can try to lower familyLimit parameter (try 1 or 1.5) if this is the case. For a single parent family, you might need 5-8 offspring to call the missing parental genotype. If you have halfsib families, they might help. Also the parameter ignoreParentOrder in ParentCall2 can be tried but that...
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Dear pasi, The VCF file contains 6715 samples, with over 4000 individuals whose sample IDs can be found in pedigree.txt. There are more than 1000 families, each of which includes parents who have at least one genotype and their offsprings also have genotypes. I am unsure if it is problematic for only the father or mother to be genotyped in the parents' case. In the screenshot I provided above, the familyID is LL14CLA17701435_LL22RK917700771. Among them, LL22RK917700771 has a genotype in the vcf file,...
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The VCF file contains 6715 samples, with over 4000 individuals whose sample IDs can be found in pedigree.txt. There are more than 1000 families, each of which includes parents who have at least one genotype and their offsprings also have genotypes. I am unsure if it is problematic for only the father or mother to be genotyped in the parents' case. In the screenshot I provided above, the familyID is LL14CLA17701435_LL22RK917700771. Among them, LL22RK917700771 has a genotype in the vcf file, while...
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The VCF file contains 6715 samples, with over 4000 individuals whose sample IDs can be found in pedigree.txt. There are more than 1000 families, each of which includes parents who have at least one genotype and their offsprings also have genotypes. I am unsure if it is problematic for only the father or mother to be genotyped in the parents' case.
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Dear chinj cheung, Are you sure that the individual names match in your pedigree and vcf? If not, ParentCall2 will give a warning that the individual(s) are not found and are set to all missing... This would explain all 1s (missing) in your data. ParentCall2 should read GT field if it does not find PL or GL. Cheers, Pasi
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Dear Julien, JoinSingles2All lists also alternative linkage groups with their LOD scores. So marker is put into LG 34 with LOD=23.8 but it could be in 3 or 4 (with much lower LOD, < 5). This information is not used by other modules but sometimes it is good to check. It can be useful for example when analysing very small datasets (say 8-20 individuals). Cheers, Pasi
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Hello Pasi, Not an issue this time as all is working fine. I juste have a question on JoinSinglesAll Output. What are the numbers after the linkage group ID for the marker integrated in a new linkage group as in this example : 34 0 34 23.811889455274443 3 4.410338025559511 4 3.3456959964294652 Are they LODscore ? Is the ordering indicative of what should be kept ? Best regards, Julien.
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When lod=1, the values of theta are 0.08, 0.02, and 0.04. At this time, there are still only two LGs.
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Hi Pasi! I used ParentCall2 to convert a .vcf.gz file to data.call.gz, but I noticed that most of the values in data.call.gz are 1. I'm not sure what the problem is. The .vcf file was generated from chip genotypes using plink, so it only contains FMT/GT information and does not include likelihood values. The most important thing is that I only got two LGs by SeparateChromosomes2（lod=10 theta=0.08）; but my family has 1483； Thanks, chinj cheung
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Lep-MAP3 updated /binary+code.zip
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Rastas Pasi M A committed [6a3e86] on Code
ParentCallPloidy
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Dear Pasi, Thanks for your answers. yours sincerely chinj cheung
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Dear chinj cheung, Yes, you should include halfSibs=1 to ParentCall2 if you have shared parents. You can add the same grandparent in multiple families, just add the different family ID for each column with the same grandparent. Lep-MAP3 does not use the information of same grandparents, it is handled the same way whether the grandparents are unique to a family or not. Cheers, Pasi
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Dear Pasi, Thank you for your response. The ped12.txt file you provided in the attachment seems to be the fourth format mentioned. When executing ParentCall2, should I add the parameter halfSibs=1? I have another question regarding if both parents of P1_m1 (father), P1_f2, and P2_f3 (two mothers) are known (genotyped or ungenotyped). If I want to provide the parents of both P1_m1 (father), P1_f2, and P2_f3 (two mothers), which would be the progeny's grandfather, should the ped12.txt file be in a...
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