automatically create index files from output in bcftools

Question

[4galaxy77]

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.

Thanks.

[Bastien Hervé]

If there is an other command called bcftools index why would you want to use an option to index your file in bcftools view ?

If you want a single command line to do both you can :

/share/apps/genomics/bcftools-1.9/bin/bcftools view -O b -o $x.multiallelicIndelsRemoved.1240positions.vcf.bgz -R $variants --exclude-types indels $sample && /share/apps/genomics/bcftools-1.9/bin/bcftools index $x.multiallelicIndelsRemoved.1240positions.vcf.bgz

Do you want to keep the $x.multiallelicIndelsRemoved.1240positions.vcf.bgz file ?

Answer 1

[Kevin Blighe]

I think that you need to clear up what your file extensions mean.

With your first command, you have specified:

-O b -o $x.multiallelicIndelsRemoved.1240positions.vcf.bgz

-O b does not output a bgzipped VCF file, as your output filename ($x.multiallelicIndelsRemoved.1240positions.vcf.bgz) is implying. -O b outputs a compressed BCF, so, your output file should have the BCF extension.

After you output BCF, you simply index it with bcftools index

Take a closer look at the command line options for the commands that you aim to use.

Kevin