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

Project description

Streaming Pileupy Documentation Status Updates

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


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


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


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.

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