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