java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R reference.fasta -I input.bam -o output.bam -U ALLOW_N_CIGARS
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Outputs | |||
| --out  -o | stdout | Write output to this BAM filename instead of STDOUT | |
| Optional Flags | |||
| --doNotFixOverhangs | false | do not have the walker hard-clip overhanging sections of the reads | |
| Advanced Parameters | |||
| --maxBasesInOverhang  -maxOverhang | 40 | max number of bases allowed in the overhang | |
| --maxMismatchesInOverhang  -maxMismatches | 1 | max number of mismatches allowed in the overhang | |
| --maxReadsInMemory  -maxInMemory | 150000 | max reads allowed to be kept in memory at a time by the BAM writer | |