Question: How to combine a multi sample VCF from multiple sample VCF and interpret a multi sample vcf of bacterial genome?
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gravatar for S AR
4 weeks ago by
S AR50
Pakistan
S AR50 wrote:

I used GATK HaplotypeCaller for Variant calling of 2300 MTB strains. Now i want to make it a multi Sample VCF.

I used CombineVariants but im comfuse that either this is correct or not.

Each of my VCF is isolated means 1 VCF from one individual sample. But GATK says: CombineVariants can be used for combine variant calls that were produced from the same samples but using different methods, for comparison.

But my Variant files are from different samples. I just want to make a multi VCF for comparison purpose of each strains variants. The VCF file generated from CombineVariant is :

Mutltisample.vcf I'm not sure is it giving the proper results?

And how to interpret this union.vcf. Like in GT column it is giving ./. what does that means? and its a haploid genome so the GT should contain a single value but few columns are representing the 1|0, 0|1...

Can anyone help?

Thank you

variant calling gatk vcf • 128 views
ADD COMMENTlink modified 4 weeks ago by Pierre Lindenbaum117k • written 4 weeks ago by S AR50
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gravatar for Raony Guimarães
4 weeks ago by
Dublin / Ireland
Raony Guimarães960 wrote:

You could merge the files with bcftools:

bcftools merge -O z -o merged.vcf.gz sample1.vcf.gz sample2.vcf.gz

ADD COMMENTlink written 4 weeks ago by Raony Guimarães960

command not working!

ADD REPLYlink written 4 weeks ago by S AR50
0
gravatar for Pierre Lindenbaum
4 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

But GATK says: CombineVariants can be used for combine variant calls that were produced from the same samples but using different methods, for comparison.

yes CombineVariants can merge vcf with the same samples (--genotypeMergeOptions PRIORITIZE ) but in your case, you need to use the option --genotypeMergeOptions REQUIRE_UNIQUE

Require that all samples/genotypes be unique between all inputs.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Pierre Lindenbaum117k
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