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interpretartion of a vcf file

Hello,

I'm currently analyzing a diploid organism and utilizing minipileup for variant calling ( https://github.com/lh3/minipileup ). Occasionally, I encounter a genotype represented as 3/0. Could you explain what this signifies? Is it typical to observe such a profile in this context?

calling genotype ont variant diploid
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written by samuelkalandarov2002 • samuelkalandarov2002

Is it typical to observe such a profile in the context of diploid organism ?

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written by samuelkalandarov2002 • samuelkalandarov2002

yes if there is more than one sample genotyped.

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written by Pierre Lindenbaum Pierre Lindenbaum

In my case , there is only one sample : here is an example of a some variants generated using minipileup :

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1

ref1 1121 . G A,C,T,GT,GTA 75 . . GT:ADF:ADR 0/1:2298,62,5,4,6,1:2312,13,8,23,3,2

ref1 1122 . TA AA,CA,GA,T,TGA 89 . . GT:ADF:ADR 0/2:2321,1,7,1,78,2:2310,5,82,12,3,3

ref1 1123 . ATT A,AT,GTT,ACTT,ATTT 318 . . GT:ADF:ADR 0/2:1917,6,314,32,4,11:2429,1,4,7,1,14

ref1 1124 . TTAC ATAC,CTAC,T,TC,TATAC,TCTAC,TTGTAC 55 . . GT:ADF:ADR 0/2:1992,2,44,3,2,9,11,1:2419,3,11,1,4,1,13,1

ref1 1125 . TACG AACG,CACG,GACG,T,TG,TCG,TCACG 75 . . GT:ADF:ADR 0/2:2393,16,17,1,8,8,15,2:2328,8,58,25,1,1,2,5

ref1 1126 . ACGG A,AG,AGG,CCGG,GCGG,TCGG,ACCGG 389 . . GT:ADF:ADR 0/3:1960,4,12,367,33,15,35,5:2382,4,2,22,1,10,3,3

ref1 1422 . CA AA,C,GA,TA,CTA,CATA,CATGAGGA 138 . . GT:ADF:ADR 0/4:2384,8,1,13,10,1,4,5:2254,2,13,32,128,1,2,10

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written by samuelkalandarov2002 • samuelkalandarov2002

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