hfan

Hi Pasi, I am working on two families. For family one, I got very nice results at the SeparateChromosomes2 stage. I decided on which lodLimit to use by the lowest number where the first group (1) mainly goes to one chromosome, and I get the same number of major LGs as the number of chromosomes in my genome, with a one-on-one relationship. However, I cannot get such glear pattern for family two. If I use the same rule for lodLimit, I end up with not enough number of LGs. Then if I continue to run...

Hi Pasi, The FitStepFunction worked really well! Thank you! I was reinventing the wheel by doing some iterative loess smoothing... One quick question, what is the last line of FitStepFunction's printscreen saying about Squeeze map? e.g. here is from one of my chromosome: java -cp ~/build/lep-anchor-code/bin FitStepFunction map=order.txt autodetecting noChromosome=1 The most abundant contig is chr1 with 54888 markers +orientation 37811 -orientation 3443 Using + orientation Squeeze map 0->57 1377->1377...

Hi Pasi, The FitStepFunction worked really well! Thank you! I was reinventing the wheel by doing some iterative loess smoothing... One quick question, what is the last line of FitStepFunction's printscreen saying about Squeeze map? e.g. here is from one of my chromosome: java -cp ~/build/lep-anchor-code/bin FitStepFunction map=order.txt autodetecting noChromosome=1 The most abundant contig is chr1 with 54888 markers +orientation 37811 -orientation 3443 Using + orientation Squeeze map 0->57 1377->1377...

Hi Pasi and dear users, I wanted to phase my vcf using SHAPEIT and it requires a genetic map. The first few lines of the example file looks like this: position COMBINED_rate(cM/Mb) Genetic_Map(cM) 61795 0.3516610754 0 63231 0.3500036909 0.0005026053001324 63244 0.3494018702 0.000507147524445 63799 0.3501262382 0.000701467586646 64150 0.3558643956 0.0008263759895016 64934 0.3567249058 0.0011060483156488 65288 0.3633379498 0.001234669949878 66370 10.0482361599 0.0121068614748898 The genetic map constructed...

Hi Pasi, Thank you very much for the reply. OK now I understand why my F1 data wasn't used since there are no grandparents for them. However they are also not selfing data. So I guess the only way to include them is to not use any phasing information and let the program try all four possibilities, in a separate map? Noted "that male and female map positions make sense only on non-selfing crosses (F1 and F2).". Since my species is actually hermaphrodite and I do not expect any achiasmatic meiosis,...

Hi Pasi, Thank you very much for the reply. OK now I understand why my TS1 data wasn't used since there are no grandparents for them. However they are also not selfing data. So I guess the only way to include them is to not use any phasing information and let the program try all four possibilities, in a separate map? Noted "that male and female map positions make sense only on non-selfing crosses (F1 and F2).". Since my species is actually hermaphrodite and I do not expect any achiasmatic meiosis,...

Hi Pasi, In my current dataset, I have several "families" and yes some of them are selfing data, but there are also crossings between F1s. Please see a demo.ped file attached: F1: Grandparents and several F1s including P1 and P2. F2_1: crossing between P1 and P2 where P1 is male (pollen) and P2 is female. F2_2: still crossing between P1 and P2 where P2 is male (pollen) and P1 is female. Here I added duplicated P1 and P2 in the vcf (P1.dup and P2.dup) so their sex code does not conflict with P1 and...

Hi Pasi, In my current dataset, I have several "families" and yes some of them are selfing data, but there are also crossings between F1s. Please see a demo.ped file attached: F1: Grandparents and several F1s including P1 and P2. F2_1: crossing between P1 and P2 where P1 is male (pollen) and P2 is female. F2_2: still crossing between P1 and P2 where P2 is male (pollen) and P1 is female. Here I used P1.dummy and P2.dummy so their sex code does not conflict with P1 and P2 in F2_1. F2_3: selfing of...