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The output SAM/BAM file is also required, [[#output File (--out)|output File (--out)]].
The output SAM/BAM file is also required, [[#output File (--out)|output File (--out)]].
Recommended usage with Recalibrator:
/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 Recalibrator:
/usr/cluster/bin/bam dedup --in ${INPUT}.bam --out ${OUTPUT}.bam --force --oneChrom
= Usage =
= Usage =
