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Identify split reads in given chromosomal regions

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Split read hunter

Travis-CI

Author Haibao Tang (tanghaibao)
Email htang@humanlongevity.com
License Restricted

Description

Identify split reads and read pairs in a particular region.

Installation

  • Checkout a copy of Splithunter and install:
git clone --recursive https://github.com/tanghaibao/splithunter
cd src && make && cd ..

Usage

  • Run batch jobs in HLI_bams.csv:
python splithunter_run.py HLI_bams.csv --workdir hli --locus TRA
  • Collect results into a TSV file:
python splithunter_report.py hli/*.json --tsv hli.splithunter.tsv

Build custom database

The default regions includes TRA, TRB, TRG, IGH, IGK, IGL. If other regions are desired, use BuildDB to build BWA indices by specifying the reference genome (e.g. hg38.upper.fa).

  • You can build your custom BWA indices using:
BuildDB src/data/TR_IG.bed -r ~/projects/ref/hg38.upper.fa

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Identify split reads in given chromosomal regions

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