svtyper¶

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.

Environment Variables¶

HPC_SVTYPER_DIR - installation directory
HPC_SVTYPER_BIN - executable directory

Categories¶

biology, genomics, sequencing