SVIndelGenotyper was employed for analyzing the error profiles of indels and structural variants in deep sequencing data.
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SVIndelGenotyper depends on python >= 3.9.9
> git clone https://github.com/stjude/SVIndelGenotyper.git
> cd SVIndelGenotyper
> ./make_install.sh
SVIndelGenotyper has 2 subcommands:
indelgenotype indels for sequencing data (WGS/WES/RNASeq)svgenotype SVs for sequencing data (WGS)
> python SVIndelGenotyper.py indel testIndel.tsv
> python SVIndelGenotyper.py sv testSV.tsv
Shao Y, Tran Q, Feng Y, Kolekar P, Liu Y, Liang Z, Fan L, McBride A, Jones T, Cameron A, Mulder H, Ji L, Huang BJ, Klco JM, Meshinchi S, Zhang J, Carroll WL, Loh ML, Easton J, Brown PA, Ma X. Analysis of error profiles of indels and structural variants in deep-sequencing data. Cell Genom. 2026 Feb 11;6(2):101082. doi: 10.1016/j.xgen.2025.101082. Epub 2025 Dec 2. PMID: 41338220; PMCID: PMC12903382.
- Yanling.Liu[AT]stjude.org
- Pandurang.Kolekar[AT]stjude.org
- Xiaotu.Ma[AT]stjude.org
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