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.txtBase 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.
1 maintainer
Metadata
1 maintainer
Release files for streaming-pileupy 0.5.7
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