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+ document how to run bcftools commands from pysam #1275

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+ document how to run bcftools commands from pysam #1275

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19 changes: 19 additions & 0 deletions doc/usage.rst
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Expand Up @@ -172,6 +172,25 @@ Note that this means that output from commands which produce output on
stdout will not be available. The only solution is to run samtools
commands through subprocess.

=====================================
Using bcftools commands within python
=====================================

Commands available in `bcftools <https://samtools.github.io/bcftools/>`_ are also available as simple
function calls, but they are invoked slightly differently from `samtools <https://www.htslib.org>`_.
Command line options are also provided as arguments. For
example::

import pysam.bcftools as bcftools
bcftools.reheader("-s", "samples.txt", "-o", "out.vcf.gz", "in.vcf.gz", catch_stdout=False)

corresponds to the command line::

bcftools reheader -s samples.txt -o out.vcf.gz in.vcf.gz

If the ``catch_stdout=False`` option is not specified, then the output of the
`bcftools <https://samtools.github.io/bcftools/>`_ command will be returned as a variable

================================
Working with tabix-indexed files
================================
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