3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→How to use it
The input SAM/BAM file ([[#input File (--in)|--in]]), the output SAM/BAM file ([[#output File (--out)|--out]]), and the reference file ([[#Reference File (--refFile)|--refFile]]) are required inputs.
The input SAM/BAM file ([[#input File (--in)|--in]]), the output SAM/BAM file ([[#output File (--out)|--out]]), and the reference file ([[#Reference File (--refFile)|--refFile]]) are required inputs.
Recommended usage with Deduper:
/usr/cluster/bin/bam dedup --recab --in ${INPUT}.bam --out ${OUTPUT}.bam --force --refFile ${REF} --dbsnp ${DBSNP} --skipFit --oneChrom --storeQualTag OQ --maxBaseQual 40
Recommended usage without Deduper:
/usr/cluster/bin/bam recab --in ${INPUT}.bam --out ${OUTPUT}.bam --refFile ${REF} --dbsnp ${DBSNP} --skipFit --storeQualTag OQ --maxBaseQual 40
= Usage =
= Usage =
