Activity for Felix
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Felix posted a comment on discussion General Discussion
Dear Pasi, Where is the parameter proximityScale ? I can ont find it in java -cp Filtering2.
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Thank you for your help, Pasi. And another question is : how does lepmap3 calculate the number of recombinations for each offspring? I didn't find this content in your paper of lepmap3. Is it estimated by calculating the recombination rate of each chromsome ? If so, how to convert "rate" to "number" ?
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Hi Pasi, Thanks for your software! Now I have a problem about the genetic map of half-sib family. My half-sib family (one same father and two mothers) includes two offspring populations and I filtered the two VCFfile respectively. So the two offspring populations have some different sites and some common sites. When I build the map, I need to use their common sites or all the sites in the two populations? cross1(male×female1) variation number: 58000 cross2(male×female2) variation number: 106000 common...
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Hi Pasi, Thank you for your help, I have constructed a nice map. For another family, I got some problems: 1. After OrderMarkers2, I find some LGs pointing the same chromosome. For example, markers of LG1 and LG2 both come from CHR6, makers of LG3 and LG4 both come from CHR4. I want to merge LG1 and LG2 to one linkage map instead of giving up one of them. I read your previous posts, you said they can manually splice two LGs. But how do I calculate the genetic distance of the gap between two LGs, because...
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Thank you Pasi， I have solved this problem, Problem is that, the outfile of bcftools 'concat' will cause this bug, but the commond of vcftools concat will report no error. Wish this can help others. Best wish, Felix
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Hi Pasi, I got a bug when I use ParentCall2 to convert a vcf file (915765 Sites; 2600MB) to data.call. But there is a problem: No grandparents present in family F Number of individuals = 82 Number of families = 1 java.lang.ArrayIndexOutOfBoundsException: 8 at DataParser$VCFParser.parseNext(DataParser.java:511) at DataParser.getNextLine(DataParser.java:686) at DataParser.getNextLine(DataParser.java:650) at ParentCall2.callParents(ParentCall2.java:155) at ParentCall2.main(ParentCall2.java:1019) Error...
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Dear Pasi, Thank you for your Lep-Map3. When I do some tests for chr1 with one family (parents and 80 offspring individuals), I got 24176 snps after SeparateChromosomes2 Module on LG1, and then I put them into OrderMarker2 Module. My questions is: 1. Does the OrderMarker2 Module have same function as 'maxDistance=NUM' of OrderMarker Module in LepMAP2, maxDistance can set the maximum recombination ratio. 2. As question 1, does the OrderMarker2 Module have same function as ''removeDuplicates" of OrderMarker...
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Hi Pasi， I got the problem, I use 'nohup' for 'OrderMarkers2', this made some Process information add to the final file, after delete these information, LMPlot run. Thank you for your reply. Cheers, Felix
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Hi Pasi, This is the order3.txt, thank you for your help! #java OrderMarkers2 map = maplod5size150.txt data = data.call chromosome = 1 numThreads = 20 useKosambi=1 numMergeIterations=1 randSeed=-5037844475770721480 Loading file No grandparents present in family F Number of individuals = 82 Number of families = 1 File loaded with 42686 SNPs Number of individuals = 82 excluding grandparents Number of families = 1 Number of LGs = 1 Number of markers = 24176 Setting dataScale to 0.0033090668431502318...
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Hi Pasi, I have a same problem in LMPlot, java -cp /home/share_data1/lvchf/software/lepmap/bin/ LMPlot order3.txt > order1.dot java.lang.NegativeArraySizeException at LMPlot.loadPrints(LMPlot.java:171) at LMPlot.main(LMPlot.java:301) I have about 20000makers, do you kown what could be causing this error?
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