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, 19:54, 19 September 2012
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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)]]. |
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| + | Recommended usage with Recalibrator: |
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| + | /usr/cluster/bin/bam dedup --recab --in ${INPUT}.bam --out ${OUTPUT}.bam --force --refFile ${REF} --dbsnp ${DBSNP} --skipFit --oneChrom --storeQualTag OQ --maxBaseQual 40 |
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| + | Recommended usage without Recalibrator: |
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| + | /usr/cluster/bin/bam dedup --in ${INPUT}.bam --out ${OUTPUT}.bam --force --oneChrom |
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| = Usage = | | = Usage = |