I need to call variants on a large number of reads using both
BCFTools. Both of these variant calling tools use
mpileup file as input to call the variants.
VarScan2 command is straightforward, as we can specify the
mpileup file as a command parameter. The problem is,
mpileup to be piped from another command and I cannot find an input parameter to specify a
mpileup file that already exists (the one used with
VarScan2). It seems horribly inefficient to run the same command twice instead of reusing the file obtained from previous step (especially because generating
mpileup takes a substantial amount of time on my computer).
Is there a way to reuse an existing
mpileup file with
I am using
Nextflow to run my pre-processing pipeline, so could it be possible that I can pipe an input channel with
mpileup into the
I also tried doing
cat file.mpileup | bcftools call ... but this does not seem to work.
cat file.mpileup | bcftools call ... does work, which would be a solution to this question, however, answers offer other, even more elegant, solutions.