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hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
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How to merge the vcfs from different samples? #102

Closed verne91 closed 5 years ago

verne91 commented 5 years ago

Hello,

I have got the svtyper results from different samples. How can I merge the vcfs into one vcf?

I found vcf_paste.py under scripts folder. But I don't find the usage for it.

Thank you!

abelhj commented 5 years ago

You can find an example workflow here. Essentially, you will want to run svtools lsort and svtools lmerge to merge the calls across samples. Then you can re-genotype the merge sites in all samples with svtyper, and paste the resulting vcfs together with svtools vcfpaste.

https://github.com/hall-lab/svtools/blob/master/Tutorial.md https://github.com/hall-lab/svtools/blob/master/Tutorial.md

Thanks, Haley

On Apr 1, 2019, at 9:18 AM, Chen Sun notifications@github.com wrote:

Hello,

I have got the svtyper results from different samples. How can I merge the vcfs into one vcf?

Thank you!

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