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Problem in merging multiple samples VCF file obtained from Structural variant caller Lumpy

Hello everyone,

I ran lumpy Sv caller for individual samples to call large structural variants. I ran SVtyper for finding the genotype. I want to combine multiple samples into 1 VCF with their respective genotype calls. I tried to install SVtools to merge the multiple samples but SVtools installation is creating a problem. I tried running SURVIVOR to combine multiple VCF files but SV caller results don't have the genotypic information due to which it creates a lot of NA values. I tried merging the VCF files through bcftools for multiple samples and am thinking to even merge the genotype VCFs of multiple samples through bcftools. Would this approach be correct? Secondly am facing issues with filetring large structural variants. How should I determine the artifacts vs true variants when filtering the Structural variants. I want to filter the variants by genotype based on genotype as 0/0 for control and the cases being positive genotype. What parameters do we consider when filtering SV's?

sv variant-calling vcf
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updated by GenoMax 16K • | written by sardana.thakur.prachi 0

1 answer

You may also want to try OctopuSV. We developed it for merging and comparing SVs across multiple samples as well as multiple callers.

For your case, the sample mode can merge equivalent SVs across samples while keeping track of which sample supports each event, which may be more useful than simply combining the VCFs with bcftools merge.

For example:

octopusv merge -i sample1.svcf sample2.svcf sample3.svcf --mode sample --sample-names Sample1,Sample2,Sample3 --union -o cohort.svcf

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written by Qingxiang 2

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