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Use GATK to revert an aligned BAM to an unaligned BAM
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| # USAGE: sh revert_bam.sh <sample name> | |
| # Assumes GATK is on the path. Based on https://gatkforums.broadinstitute.org/gatk/discussion/6484#latest%23top | |
| gatk RevertSam \ | |
| -I=$1.bam \ | |
| -O=$1.unmapped.bam\ | |
| -SANITIZE=true \ | |
| -MAX_DISCARD_FRACTION=0.005 \ | |
| -ATTRIBUTE_TO_CLEAR=XT \ | |
| -ATTRIBUTE_TO_CLEAR=XN \ | |
| -ATTRIBUTE_TO_CLEAR=AS \ | |
| -ATTRIBUTE_TO_CLEAR=OC \ | |
| -ATTRIBUTE_TO_CLEAR=OP \ | |
| -SORT_ORDER=queryname \ | |
| -RESTORE_ORIGINAL_QUALITIES=true \ | |
| -REMOVE_DUPLICATE_INFORMATION=true \ | |
| -REMOVE_ALIGNMENT_INFORMATION=true |
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