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?