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comparison of variants between WGS samples

I never worked on such specific task so there may be a simple solution that I don't know, I need to find the rate of similarity and find out what are the differences between 2 WGS human samples. Let's say I want to know what variants are specific of sample1, what are specific of sample2 and what are shared between sample1-sample2.

I run GATK HaplotypeCaller on them and I have the GVCF results. How can I compare them? Is there any software out there able to find out differences between samples?

Thank you very much in advance for any help!

wgs human gatk differences variants
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updated by harold.smith.tarheel harold.smith.tarheel • written by cocchi.e89 cocchi.e89

1 answer

VCFtools '--diff' command can be used to compare VCFs for unique and shared variant calls.

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written by harold.smith.tarheel harold.smith.tarheel

OP has GCVF's. VCFtool can handle those?

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written by GenoMax GenoMax

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