Difference between revisions of "Svtyper"
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Latest revision as of 14:04, 3 October 2022
Description
SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data. Users must supply a VCF file of sites to genotype (which may be generated by LUMPY) as well as a BAM/CRAM file of Illumina paired-end reads aligned with BWA-MEM. SVTyper assesses discordant and concordant reads from paired-end and split-read alignments to infer genotypes at each site. Algorithm details and benchmarking are described in Chiang et al., 2015.
Environment Modules
Run module spider svtyper to find out what environment modules are available for this application.
System Variables
- HPC_SVTYPER_DIR - installation directory
Additional Information
NOTE: This program uses a no-longer supported version of Python (2.7). Some functions of newer editions of python may not be available.
Citation
If you publish research that uses svtyper you have to cite it as follows:
C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth 12, 966–968 (2015). doi:10.1038/nmeth.3505.
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html