filtering

Recurrent somatic indels

Except for a few known hotspots, true somatic indels rarely recurr.

Ocurrence annotation

When multiple RNAIndel output VCF files are generated from the same cohort, occurrence with in the cohort is annotated in INFO field.

rnaindel CountOccurrence --vcf-list vcf_paths.txt -r reference.fa

Options

• --vcf-list file containing paths to RNAIndel output VCF files (path/line) (required)
• -r reference genome FASTA file (required)
• --out-dir output directory for annotated VCF file. The input file dir is used if not specified.
                      (file name will not be changed after annotation)