indelPost

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 called differently by 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
• genotyping indels (the alleles may be aligned differently in the target BAM file)

Visit documentation for detail.

To install (require Linux with Python>=3.6 pre-installed):

pip install indelpost --no-binary indelpost --no-build-isolation

Troubleshoot

If you have installation errors related to ssw-py, try installing separately by:

pip install ssw-py

or from source
or from tar.

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 pysam
pip install indelpost --no-binary indelpost --no-build-isolation

Reference

Hagiwara K et al. (2022) indelPost: harmonizing ambiguities in simple and complex indel alignments. Bioinformatics

Contact

• kohei.hagiwara[AT]stjude.org