So we have several flow cells worth of indexed samples generated from targeted resequencing and I want to merge all of the variant calls for all samples with the ability to distinguish between no-call and reference-call for all samples. Would I be best advised to
a) merge all the bam files and generate the vcf from there
or
b) take all the individual sample vcfs and merge them with vcftools
?
a) merge all the bam files and generate the vcf from there
or
b) take all the individual sample vcfs and merge them with vcftools
?