Entering edit mode
10.7 years ago
ElCascador
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30
Hi !
I received VCF files for 3 individuals from exom sequencing. One line is as this :
1 859913 rs112703963 A A 104 . DN=132;DA=A/G;GM=none;FG=upstream-gene;FD=upstream-variant-2KB;CP=0.927;CG=-3.770;AA=G;DV=by-frequency,by-cluster;RM=(CCG)n;DSP=416;CPG=858971-861632 GT:PL:DP:GQ 0/1:139,0,186:23:99 0/0:0,54,255:18:58 0/0:0,48,255:16:52
What was bothering me is that the ALT base is the same as the REF base. Only one out of the 3 individuals is heterozygote for G, which seems to be the ancestral state from the chimp (AA and DA fields)
They used samtools mpileup to generate those VCF, then filtered polymorphism with vcftools.
Somebody knows how the ALT base is selected and the story with the ancestral chimp base ?
Cheers. PS : Any hint on how can i format properly my text ? Is it normal HTML tags ? Thanks
