I'm a bit blocked with an update of

BCFTOOLS_MPILEUP

I would like to use the

-C alleles

option in the

call

sub-command in

bcftools \\
        mpileup \\
        --fasta-ref ${fasta} \\
        ${args} \\
        ${bam} \\
        ${intervals_mpileup_cmd} \\
        ${mpileup} \\
        | bcftools call --output-type v ${args2} ${intervals_call_cmd} \\
        | bcftools reheader --samples sample_name.list \\
        | bcftools view --output-file ${prefix}.vcf.gz --output-type z ${args3}

To do so, I need to have a bed file for the

-T

intervals file. The issue is that the intervals file for the

call

sub-command need a fourth column with

REF,ALT

whereas the one for the

mpileup

subcommand only need the first three columns. Here are the possibility: • use only one file as intervals input that would be used for both sub-command but this would force every usage to use a four column bed file • use two file one for each subcommand (as shown in example), but then you need to duplicate the file and rename it to avoid name conflict • use only one file and a flag to tell to which command associate the intervals flag What are your thoughts?

You can avoid the issue with having to rename them by getting the module to do with that via stageAs