I thought this command would give me a new vcf file without the individuals in the text file:
vcftools --gzvcf mergedPF.vcf.gz --remove listPnsToRemoveFromMergedVcf.txt --out filtMergedPTrios
Instead it gives me an index file and a log file.
I must be missing some obvious point. I want to filter out some individuals from the gvcf file for a new gvcf file. What is the fastest way of doing this? Like vcf-subset?
--recode fixed it but the info field is gone.
vcf-subset -c pnsToKeepInCpTrio.txt copyPhasedCpTrio.vcf.gz > keptPnsFromCpTrio.vcf
worked also retaining info.