UMI-VarCal
Description
Software for analyzing BAM/SAM files produced by an Illumina MiSeq sequencers using UMI (Unique Molecular Identifiers). The software starts by building a pileup based on the regions specified in the BED file. This software integrates an extraction tool that can be used to extract UMI tags from the start of the reads. The software has also a calling tool for calling variants and that outputs the results under VCF format. Although SAM files generated by an Illumina MiSeq sequencers were used to develop this tool, it should work on BAM/SAM files generated by any other sequencer as long as they respect the Sequence Alignment/Map Format Specification.
Availability
version 2.4.3
Use
module add umi-VarCal-2.4.3
python3 umi-varcal.py extract -h
python3 umi-varcal.py call -h
Documentation
https://gitlab.com/vincent-sater/umi-varcal-master