NGS pipeline for the detection of somatic variation (SNVs, Indels and CNVs) from capture-based libraries. Version 1.0.0 is not validated for CNV or Fusion Detection. The validation documentation and SOP can be found on QPulse:
LP-GEN-PanCanAnlyss
Useage:
qsub 1_SomaticEnrichment.sh
command must be issues inside sample directory; which contains:
{samplename}.variables file
SomaticEnrichmentLib-{version} library
{sample}.fastq.gz files
The no template control must be named "NTC" in the SampleSheet.csv.