From Genome Analysis Wiki
filter option on the bam executable writes the alignments filtering them by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high.
Required Parameters: --in : the SAM/BAM file to be read --refFile : the reference file Optional Parameters: --noeof : do not expect an EOF block on a bam file.
./bam filter --in <inputFilename> --refFile <referenceFilename> [--noeof]
- 0: all records are successfully read and written.
- non-0: at least one record was not successfully read or written.
The following parameters are available. Ones with "" are in effect: Input Parameters --in [testFiles/testFilter.sam], --out [-], --refFile [testFiles/chr1_partial.fa], --noeof, --qualityThreshold , --defaultQualityInt , --mismatchThreshold [0.49] open and prefetch reference genome testFiles/chr1_partial.fa: done. Number of Reads Clipped by Filtering: 8 Number of Reads Filtered Due to MismatchThreshold: 1 Number of Reads Filtered Due to QualityThreshold: 2