Is there way to combine these samtools commands:

1. `samtools view -h -F 0x10 <bam>` 

2. `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.

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>

