Identify split reads and read pairs in a particular region.

• Checkout a copy of Splithunter and install:

git clone --recursive https://github.com/tanghaibao/splithunter
cd src && make && cd ..

• 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

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