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wdecoster / surpyvor

A python wrapper around SURVIVOR
MIT License
19 stars 1 forks source link

extracting variants list unique to a specific group #18

Closed dKlee99 closed 3 years ago

dKlee99 commented 3 years ago

Hi, thanks for providing this wonderful packages!!

Is it possible to extract 99 variants list (in vcf/bed or any possible forms) that is only present in T15_kmers as well as the type of SV (INS, DEL, INV etc) there are?

Thank you very much for your help in advance ! DK image

wdecoster commented 3 years ago

Hi DK,

Thanks for your question. Yes, that should be possible, although not immediately using a surpyvor command. You could use either --keepmerged with surpyvor venn to save the merged VCF when creating the plot, or just use surpyvor merge to merge the datasets. You can then query the VCF using e.g. the SUPP_VECTOR or a bcftools command to extract those variants that fit your condition.

Cheers, Wouter

dKlee99 commented 3 years ago

Hi, Thank you so much for your reply!

Would it be possible to filter out by setting genotype of normal and T15 to ./. and 0/0 to see only T15_kmers (somatic variations) as well? I couldn't really understand the part "SUPP_VECTOR or a bcftools command to extract those variants that fit your condition." Thank you so much!

Kind regards, DK

dKlee99 commented 3 years ago

Hi DK,

Thanks for your question. Yes, that should be possible, although not immediately using a surpyvor command. You could use either --keepmerged with surpyvor venn to save the merged VCF when creating the plot, or just use surpyvor merge to merge the datasets. You can then query the VCF using e.g. the SUPP_VECTOR or a bcftools command to extract those variants that fit your condition.

Cheers, Wouter

Did you mean use bcftools to filter out SV that is present in other two groups by genotype?

wdecoster commented 3 years ago

That should work yes, from the merged VCF.

dKlee99 commented 3 years ago

Thank you very much!