Flagging Independently - cancerit/cgpCaVEManPostProcessing GitHub Wiki
Filtering CaVEMan results can be run separately to the cgpCaVEManWrapper process. The following is an example command:
cgpFlagCaVEMan.pl -i <file_for_flagging.vcf> \
-o <output.vcf> \
-m tumour.bam \
-n normal.bam \
-ref <path to reference index .fai file> \
-b <directory containing flagging bgzipped and tabixed bed files> \
-g <path to bgzipped tabixed germline indel bed file> \
-umv <directory containing unmatchedNormal.bed.gz unmatched normal bed file> \
-ab <directory containing flagging bgzipped and tabixed bed annotation related files> \
-s <species> \
-t <seq_type (genome|genomic|WGS|pulldown|exome|WXS|followup|AMPLICON|targeted|RNA_seq)> \
-flagConfig <flag.vcf.config.ini> \
-flagToVcfConfig <path to flag.to.vcf.convert.ini>