Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
normal_bam
Coordinate sorted BAM/CRAM/SAM file from normal tissue
*.{bam,cram,sam}
normal_bai
Index for coordinate sorted BAM/CRAM/SAM file from normal tissue
tumor_bam
Coordinate sorted BAM/CRAM/SAM file from tumor tissue
tumor_bai
Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue
homopolymers
Output file from MSIsensor scan module
*.msisensor_scan.tab
versions
File containing software versions
versions.yml
txt
MSIsensor MSI final report file
*.output
MSIsensor MSI DIS report file
*.output_dis
MSIsensor MSI germline report file
*.output_germline
MSIsensor MSI somatic report file
*.output_somatic
MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
