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 variation mumber: 20000
Thanks in advance,
Felix
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You need to merge the vcf files to have same markers in both families. Maybe bcftools merge will work here? You can use the common markers but if the families are large enough, you can use markers only in one family (albeit less informative).
Maybe it could be easier to do filtering in the merged vcf only as the families are related?
Cheers,
Pasi
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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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The number and position of recombinations come from the two Viterbi paths (paternal and maternal haplotypes, 0=>1 or 1=>0 transition is a recombination) of the hidden Markov model used to calculate the likelihood. This number is converted to cM by dividing it by the number of offspring and using a mapping function between each adjacent markers.
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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 variation mumber: 20000
Thanks in advance,
Felix
Dear Felix,
Thank you for your question.
You need to merge the vcf files to have same markers in both families. Maybe bcftools merge will work here? You can use the common markers but if the families are large enough, you can use markers only in one family (albeit less informative).
Maybe it could be easier to do filtering in the merged vcf only as the families are related?
Cheers,
Pasi
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" ?
Dear Felix,
The number and position of recombinations come from the two Viterbi paths (paternal and maternal haplotypes, 0=>1 or 1=>0 transition is a recombination) of the hidden Markov model used to calculate the likelihood. This number is converted to cM by dividing it by the number of offspring and using a mapping function between each adjacent markers.
Cheers,
Pasi