Hi everyone,

I have individual vcf files of indels and want to merge them into a big one, but only extract chromosome 3,4,5,7,8 into a unified file. The list of vcf files is in round1_indel.txt.

What I did is:

bcftools merge -l round1_indel.txt -o round1_indel.vcf -r 3,4,5,7,8

However, the output is only for chromosome 3. The document file for bcftools say the -r option is separate by comma. I don't know what is the problem here. Thank you so much!