indelPost: Python library for simple and complex indels.

Author:

Kohei Hagiwara

Date:

Jan 22, 2024

Version:

0.2.3

To install:

git clone https://github.com/stjude/indelPost.git
cd indelPost
python setup.py install

Installing indelPost also installs the dependency:

• numpy>=1.16.0

• pysam>=0.15.0

• cython>=0.29.12

Note

indelPost is supported for Linux with Python>=3.6.

Contents

• Introduction
• API
  • indel processing on the reference
  • indel processing on alignment files (BAM)
• Examples
  • Equalities
  • Querying VCF file
  • Decomposing complex indels
  • Counting/Fetching indel-supporting reads
  • Annotating complex indels from simple indels
  • Integrating indel call sets
• Benchmarking
• Limited support for SNV/MNVs

• Index