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BAM filter (version 0.5.9)

Select BAM dataset:

Remove reads that are smaller than:

in bp

Remove reads that are larger than:

in bp

Keep only mapped reads:

Keep only unmapped reads:

Keep only properly paired reads:

both mapped, correct orientation, flag set in BAM

Discard properly paired reads:

Remove reads that match the mask:

e.g. 0x400, 0x2

Remove reads that have the same sequence:

up to the Nth nucleotide starting from the 5prime end. -1 means do not filter, 0 means check along the entire read, 10 would make filter reads that are unique over the first 10 nucleotides.

Remove reads that start at the same position:

Use only for low-coverage samples

Remove reads with that many mismatches:

Indels always counts as 1 regardless of length. Requires NM tag to be set.

Remove secondary alignment reads:

Remove reads flagged with 0x100

Remove reads that do not pass the quality control:

Remove reads flagged with 0x200

Remove reads that are marked as PCR dupicates :

Remove reads flagged with 0x400

Remove reads that are in any of the regions:

Remove reads that are NOT any of the regions:

Strand information from BED file is ignored:

Affects -excludebed and -includebed.

Exclude reads NOT mapped to a reference:

Exclude reads mapped to a particular reference:

e.g. chrM, or _dup chromosomes

Filter by maximum mismatch ratio:

fraction of length

Removes reads from a BAM file based on criteria.

Given a BAM file, this tool will discard reads that did not meet the selected filtering criteria The output is another BAM file with the reads not matching the criteria removed.

Note: this does not adjust tag values reflecting any filtering. (for example:: if a read mapped to two locations (IH:i:2), and one was removed by filtering, the IH:i tag would still read IH:i:2).

Currently, the available filters are:

Agument	Description
-minlen val	Remove reads that are smaller than {val}
-maxlen val	Remove reads that are larger than {val}
-mapped	Keep only mapped reads
-unmapped	Keep only unmapped reads
-properpair	Keep only properly paired reads (both mapped, correct orientation, flag set in BAM)
-noproperpair	Keep only not-properly paired reads
-mask bitmask	Remove reads that match the mask (e.g. 0x400)
-uniq {length}	Remove reads that are have the same sequence Note: BAM file should be sorted (up to an optional length)
-uniq_start	Remove reads that start at the same position Note: BAM file should be sorted (Use only for low-coverage samples)
-mismatch num	Number of mismatches or indels indel always counts as 1 regardless of length (requires NM tag in reads)
-nosecondary	Remove reads that have the 0x100 flag set
-noqcfail	Remove reads that have the 0x200 flag set
-nopcrdup	Remove reads that have the 0x400 flag set
-excludebed file.bed {nostrand}	Remove reads that are in any of the regions from the given BED file. If 'nostrand' is given, strand information from the BED file is ignored.
-includebed file.bed {nostrand}	Remove reads that are NOT any of the regions from the given BED file. If 'nostrand' is given, strand information from the BED file is ignored. Note: If this is a large dataset, use "bamutils extract" instead.
-includeref refname	Exclude reads NOT mapped to a reference
-excluderef refname	Exclude reads mapped to a particular reference (e.g. chrM, or _dup chromosomes)