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It is possible to merge gVCFs generated from the same sample but sequenced in different runs ?

Hi,

I have a set of gVCFs generated from publicly available data. It happens that some of these are from the same sample, but there are multiple runs for some of the samples.

I am wondering if it is possible to merge the gVCFs that were generated for these runs into a single gVCF which represents that sample.

Put simply, what I would like to do is this:

run_1.g.vcf + run_2.g.vcf --> sample.g.vcf

Thanks

vcf bcftools vcftools wgs
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by setantas • setantas

hum... I would call each GVCF to VCF and then merge the two files will bcftools concat --allow-overlaps --remove-duplicates

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks I will try this. Doing joint-genotyping on all these now. I'm just wondering if it is possible to use the bcftools concat function on a multisample VCF?

So, say each run VCF is part of a multisample VCF. Is there some way I can run the bcftools command you suggested without splitting the multisample VCF into each of the VCFs that I want to merge?

I am thinking maybe I would add something along the lines of bcftools view -s run1,run2 but I am not very familiar with this software.

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written by setantas • setantas

I'm just wondering if it is possible to use the bcftools concat function on a multisample VCF?

yes if they all have the same samples in the same order.

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written by Pierre Lindenbaum Pierre Lindenbaum

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