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The handling of paired-end reads assumes that the mate information in the SAM/BAM records is accurate. If a mate is not found at the expected position, an error message is printed (once per file) indicating this error. Paired-end reads whose mate cannot be found are not marked duplicate and are not used for duplicate marking of other paired-end reads. Single-end reads with the same key as paired-end reads whose mate cannot be found are still marked as duplicate. If this error is encountered, you may want to fix the mate information and reprocess the file through the deduper.
The handling of paired-end reads assumes that the mate information in the SAM/BAM records is accurate. If a mate is not found at the expected position, an error message is printed (once per file) indicating this error. Paired-end reads whose mate cannot be found are not marked duplicate and are not used for duplicate marking of other paired-end reads. Single-end reads with the same key as paired-end reads whose mate cannot be found are still marked as duplicate. If this error is encountered, you may want to fix the mate information and reprocess the file through the deduper.
Use the [[#Treat Reads with Mates On Different Chromosomes As Single-Ended (--oneChrom)|<code>--oneChrom</code>]] option to treat reads with a mate on a different chromosome as single-ended. This option is useful if you are running the deduper on just a single chromosome. The code will use less memory with this option if mates are found on different chromosomes.
With the default settings this tool should produce similar results as Picard.
Use the [[#Treat Reads with Mates On Different Chromosomes As Single-Ended (--oneChrom)|<code>--oneChrom</code>]] option to treat reads with a mate on a different chromosome as single-ended. This option is useful if you are running the deduper on just a single chromosome. The code will use less memory with this option if mates are found on different chromosomes. (Picard does not specially handle mates on different chromosomes, so the --oneChrom option may produce different results than Picard.)
Recommended usage with Recalibrator:
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
/usr/cluster/bin/bam dedup --recab --in ${INPUT}.bam --out ${OUTPUT}.bam --force --refFile ${REF} --dbsnp ${DBSNP} --oneChrom --storeQualTag OQ --maxBaseQual 40
