Greetings,
Is there a proper way to subset a gvcf file created from HaplotypeCaller? I have a large number of gvcf files from various sequence projects, including whole exome. I was trying to subset specific snp sites and run joint genotyping. My initial impulse was to use vcftools, but for whatever reason I do not see any positions in the resulting outfile (the should otherwise exist, as I have checked the input).
Perhaps a gvcf will not behave the same way for vcftools? But then is there a recommended alternative for pulling specific sites or should I write some code? Thanks.
-bwubb