Piping a bam file to samtools calmd
Is there way to combine these samtools commands:
samtools view -h -F 0x10 <bam>samtools calmd <bam_from_step_1> <ref.fasta>
I tried this:
samtools view -h -F 0x10 <bam> | samtools calmd <ref.fasta> | samtools view -bS - > <out.bam>
But it doesn't work.
1 answer
In bash you need to use - to specify that the input is coming from a pipe. You should also add the -S parameter to specify that the input is SAM (or follow the suggestion of @swbarnes2 and output BAM from view instead):
samtools view -h -F 0x10 <bam> | samtools calmd -S - <ref.fasta> | samtools view -bS - > <out.bam>
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For one thing, samtools view outputs data in .sam format, not .bam format. So if calmd requires a .bam format, add -b to samtools view top give it a bam.