interpretartion of a vcf file
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8 weeks ago

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 • 441 views
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see Genotype representation with 0, 1, 2 - what do they mean?

Could you explain what this signifies?

diploid HET genotype with the REF allele and an alternat allele (the 3rd in the ALT column)

For all samples for this variant, there is at least 3 possible ALT alternate alleles.

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

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yes if there is more than one sample genotyped.

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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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