Pasi Rastas

Dear Ana, In the data you provided earlier (test_subset.vcf), I only find 3 variants with data on more than 100 individuals. This spans over 10Mb of genome so I expect it is normal that it is difficult to analyse as it contains very little information. If the rest of the data is this sparse, there are actually about 800 markers with some information. And this information is from about 100 individuals out of over 10k individuals. From this information, my guess is that it cannot be analysed. What...

Dear Lorenzo, EstimateRecombination outputs map and recombination rate only in a grid with a constant size (parameter gridSize=1024). Cheers, Pasi

Dear Sam, Thank you for your question. The maps look about as good as they can, being build "de novo" without genome coordinates. My gut feeling is that the double lines are caused because some markers have missing/erroneous genotypes. This uncertainty of map positions can be obtained from the map intervals (parameter calculateIntervals=file), I did discuss this in detail in my Lep-Anchor paper. Basically I have suggested three ways to fix this: 1) evaluate the map in the physical order (evaluateOrder=phys_order.txt,...

Dear Ana, Thank you for your question. Please search the discussions with word "haploid", it seemed to find many relevant topics that might help you (sorry for my lazy answer). Lep-MAP3 can analyse you data, but you have to "trick" Lep-MAP3 to think the data is in one of its supported formats F1/F2/selfing cross. Anyway, I checked you pedigree and you should add two parents to your family (real parent and dummy, or grandparent(s) and dummy parents). Now the other parent is 0 that does not pass Lep-MAP3....

Dear Huan, Thank you for your question. Getting markers into right number of groups can be difficult. There are many discussion threads that might help here. First of all, always make sure that your family structure is correct! Then make sure to use distortionLod=1 (or filter distorted markers in other ways). This should make the marker assignment more robust. With 400 individuals in one family, you could use a lodLimit of about 40. And you can always use both families to assign markers as well if...

Dear Huan, The squeeze removes map positions from the map ends if there are no support for them, basically making the map start at 0cM. Cheers, Pasi

Dear Huan, Thank you for your question. Having this kind of map data is normal. My understanding is that there are transposable elements and other repeats that make some markers map into wrong chromosomes and places. This can be fixed by removing markers in the wrong chromosomes. I don't know how much such markers affect other analysis, but these stand out in linkage maps. Addition to these "jumping" markers, within chromosomes the map data is not necessary informative enough to put all markers into...

Dear Xuemei, Yes, 00 is missing data. sexAveraged=1 only puts average map position to the output maps. It does not change the algorithms in any way. The same effect can be obtained by calculate the average map position from the output of LM3 with sexAveraged=0. Cheers, Pasi