indelPost is a Python library for indel processing via realignment and read-based phasing to resolve alignment ambiguities. By importing the library, users write their own scripts to solve alignment-sensitive problems such as:
- compare/integrate indels that are differently called by multiple variant callers (e.g., complex indels).
- compare indel alignments in multiple mappings (e.g., match DNA indels to RNA-Seq for expression check).
- construct a complex indel from a simple indel by read-based phasing.
- extract reads supporting the target indel from BAM file.
- pull variant records matching the target indel from VCF file.
- count reads supporting indels by realignment.
Visit documentation for detail.
To install (require Linux with Python>=3.6 pre-installed):
pip install indelpost
or from source
git clone https://github.com/stjude/indelPost.git
cd indelPost
python setup.py install
If you get something like:
... may indicate binary incompatibility. Expected 88 from C header, got 72 from PyObject
or
AttributeError: module 'pysam.libcalignmentfile' has no attribute 'IteratorColumnAll'
try:
pip uninstall cython pysam indelpost
pip install cython
pip install pysam
pip install indelpost --no-binary indelpost --no-build-isolation
Hagiwara K et al. (2022) indelPost: harmonizing ambiguities in simple and complex indel alignments. Bioinformatics
- kohei.hagiwara[AT]stjude.org