(under development)
variantPost is a Python library for short variant processing via realignment and read-based phasing to resolve alignment ambiguities. By importing the library, users write their own scripts to solve alignment-sentive problems such as:
- compare SNVs, MNVs, and indels that may differently be called by multiple variant callers (e.g., complex indels).
- compare short variant alignments in multiple mappings (e.g., match DNA variants to RNA-Seq to check expression, where the DNA/RNA alignments may be different).
- construct a complex indel or MNV from a simple short variant by read-based phasing.
- count reads supporting the target variant from BAM file by realignment.
- pull variant records matching the target varitnt from VCF file.
variantPost supports tumor/normal-paired analyis for cancer genomics applications.
Visit documentation for detail.
variantPost requires a Linux machine with a gcc compiler supporting for c++17.
To install
pip install git+https://github.com/rawagiha/variantPost
Upon installation, cython and pysam will also be installed if not pre-installed.
variantPost internally uses the following packages. I thank the developers for making them freely available.