How do I call variants using BCFTools without piping mpileup file?

Question

I need to call variants on a large number of reads using both VarScan2 and 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, BCFTools expects 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 BCFTools?

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 BCFTools's call command?

I also tried doing cat file.mpileup | bcftools call ... but this does not seem to work.

Edit: cat file.mpileup | bcftools call ... does work, which would be a solution to this question, however, answers offer other, even more elegant, solutions.

Answer 1

Why not use tee? Please see this post.

You can write mpileup to file while also piping it to another process. For example, samtools mpileup ... | tee file.mpileup | bcftools call ...

the bcftools will run while generating the file.mpileup. After it's done, you can use file.mpileup for your VarScan2.

You can test it with the following:

touch helloworld.txt
ls | tee file.txt | grep helloworld    # output helloworld.txt
cat file.txt | grep helloworld         # output helloworld.txt

Answer 2

Bcftools and samtools both follow the very common Unix filter pattern: they read from all input files specified (as non-option plain arguments), or if there are none they read from standard input.

bcftools call is no exception:

$ bcftools call

About:   SNP/indel variant calling from VCF/BCF.
         To be used in conjunction with bcftools mpileup.
         [etc]
Usage:   bcftools call [options] <in.vcf.gz>

So you can write either of the following equivalently:

cat file.mpileup | bcftools call [options]
bcftools call [options] file.mpileup

This assumes that the file is VCF/BCF as produced by bcftools mpileup, and not actually textual “mpileup output” as suggested by the filename. If it is the latter that VarScan2 is expecting, you won't be able to share the input files between the two after all.

See this workflow example, which demonstrates bcftools call both with a pipe and a previously made input file.