BamUtil: filter

filter

The 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.

Parameters

    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.

Usage

   ./bam filter --in <inputFilename>  --refFile <referenceFilename> [--noeof]

Return Value

• 0: all records are successfully read and written.
• non-0: at least one record was not successfully read or written.

Example Output

The following parameters are available.  Ones with "[]" are in effect:

Input Parameters
 --in [testFiles/testFilter.sam], --out [-],
 --refFile [testFiles/chr1_partial.fa], --noeof, --qualityThreshold [30],
 --defaultQualityInt [20], --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