streaming-pileupy 0.5.4

Create multi-sample text-pileups of streaming SAM/BAM files.

Streaming Pileupy

Create multi-sample text-pileups of streaming SAM/BAM files.

• Free software: MIT license

• Documentation: https://streaming-pileupy.readthedocs.io.

Features

Streaming Pileupy creates a pileup of a single SAM/BAM file using the read group SM identifier to split reads by sample:

# extract sample names from read group SM tag
samtools view -H input.bam \
  | grep '^@RG' \
  | perl -pne 's/.*SM:(\S+).*/$1/' \
  | sort | uniq > sample_names.txt

# create read-group aware pileup
spileup input.bam sample_names.txt

Base quality filtering

Bases with less than a certain quality can be filtered with -Q.

Missing features

• Read beginning and end annotations in pileup output

• Deletion annotations in pileup output

• Filter output bases on BED file

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.5.0 (2020-05-05)

• Add base quality filter (-Q)

0.4.0 (2020-05-05)

• Add support for python 3.6

0.3.0 (2020-05-05)

• Add support for basic pileup functionality

0.2.1 (2020-05-04)

• First release on PyPI.