GT vardict info

[asmlgkj]

Dear professor,
Thanks a lot for such a powerful tool.
0 how can I get the vardict version from script, not from the download
1 in the GT field, why the tumor is all 0/0, but normal sample has 26 0/1, because I need to use the vcf tor pvacseq(griffithlab/pVACtools#705)
2 many STATUS=StrongLOH, the AF field is 0
vcf like this

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GT information
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I even do not know 1/0 mean
0/0 is homo ref;
0/1 ref+alt
1/1 alt+alt

[PolinaBevad]

Hello @asmlgkj!

Sorry for the late answer!
There is vardict in bioconda (and vardict-java as well), so please use it: https://bioconda.github.io/recipes/vardict/README.html

We apply genotype for somatic mode in var2vcf_paired.pl. There is a little description, can you please check? https://github.com/AstraZeneca-NGS/VarDict/blob/master/var2vcf_paired.pl#L363 You can adjust minimum frequency to consider variant as homozygous with -f option.

We apply StrongLOH if we didn't find variant in tumor (and somatic AF=0 for tumor sample then) but we found it in normal, and AF for normal is in Sample section. For StrongSomatic it is almost vice versa - we found variant in tumor but not in normal. Both cases can be 0/0 if AF is small.

Hope this helps!

[asmlgkj]

thanks a lot for your kind and helpful answer,
the GT is really much differnent from gatk and other caller.
you told me about paired mode, but if it is tumor nly mode, how can I understand the GT
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and how should I understand 1/0 in GT

[PolinaBevad]

GT is almost the same in tumor-normal and tumor-only: so 1/0 heterozygous genotype will be applied to the variants with AF between 0.5 - 0.8 and 0/1 for AF between 0.2-0.5. Really you can treat 0/1 and 1/0 as the same genotypes because they are unphased.
And AF < 0.2 is homozygous REF (0/0), AF > 0.8 is homozygous ALT (1/1).

[asmlgkj]

Thanks a lot, it is very helpful