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
Speed benchmarks¶
Speed benchmarks are available at http://warrenwk.com/streaming_pileupy/
The benchmarks are run using Airspeed Velocity:
Credits¶
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.