Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
I recently had trouble running the bcftools commands within pysam. I saw the "Using samtools commands within python" section within the documentation and thought things would behave similarly. I didn't find it to be true. I ended up finding the solution through github issue 958.
I thought it would be nice to have this bcftools feature more explicitly documented for future users.
Let me know if any additional changes are desired.
I recently had trouble running the
bcftoolscommands within pysam. I saw the "Using samtools commands within python" section within the documentation and thought things would behave similarly. I didn't find it to be true. I ended up finding the solution through github issue 958.I thought it would be nice to have this
bcftoolsfeature more explicitly documented for future users.Let me know if any additional changes are desired.