Quite a few google searches are giving me this type of command to convert VCF to BCF:
bcftools view -bS -D chr_list.txt My_mapped_reads.raw.vcf > My_mapped_reads.raw.bcf
gives view: invalid option -- 'b'
From looking at the current documentation I tried:
bcftools view My_mapped_reads.raw.vcf -Oz > My_mapped_reads.raw.bcf
Is it really as simple as the second command now or am I missing something?
please, review and validate your previous question. e.g: I took the time to answer bcftools selest sites with FILTER "PASS" or "." . If it's correct, you should validate to close it . Green mark on the left.
Sorry, I actually didn't know that was the proper workflow, closing out now!