Read clipping based on quality, position or sequence matching
java -jar GenomeAnalysisTK.jar -T ClipReads -R reference.fasta -I original.bam -o clipped.bam -XF seqsToClip.fasta -X CCCCC -CT "1-5,11-15" -QT 10
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Outputs | |||
| --out  -o | stdout | Write BAM output here | |
| --outputStatistics  -os | NA | File to output statistics | |
| Optional Parameters | |||
| --clipRepresentation  -CR | WRITE_NS | How should we actually clip the bases? | |
| --clipSequence  -X | NA | Remove sequences within reads matching this sequence | |
| --clipSequencesFile  -XF | NA | Remove sequences within reads matching the sequences in this FASTA file | |
| --cyclesToTrim  -CT | NA | String indicating machine cycles to clip from the reads | |
| --qTrimmingThreshold  -QT | -1 | If provided, the Q-score clipper will be applied | |