say i am running a command in bcftools like
/share/apps/genomics/bcftools-1.9/bin/bcftools view -O b -o $x.multiallelicIndelsRemoved.1240positions.vcf.bgz -R $variants --exclude-types indels $sample
Rather than then having to run a separate command on the output file to produce an index file:
/share/apps/genomics/bcftools-1.9/bin/bcftools index $x.multiallelicIndelsRemoved.1240positions.vcf.bgz
Is there a option that I can use in the first command which will automatically produce an index for the output file? I'm sure there must be, but I couldn't find it in the documentation.