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Samtools view -f "OR" operator possible?

Quick question:

Is it possible to do a samtools view -f XXX using a OR operator?

Say if I wanted to get all reads that were unmapped (4) or supplementary alignments (2048).

Is this possible? Because doing a 2052 is an "AND" (reads are unmapped and supplementary alignments which is impossible)

samtools
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updated by dariober dariober • written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

3 answers

using samjdk http://lindenb.github.io/jvarkit/SamJdk.html

 java -jar dist/samjdk.jar -e 'return record.getSupplementaryAlignmentFlag() || record.getReadUnmappedFlag();' in.bam
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written by Pierre Lindenbaum Pierre Lindenbaum

BamTools can do what you want, read the filter section of the tutorial. When you set multiple properties in one filter, these properties are AND-ed, and when you set multiple properties in different filters, these properties are OR-ed.

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written by h.mon h.mon

The closest I can think of is, using samtools (not tested):

samtools merge - \
    <(samtools view -u -f 4 in.bam) \
    <(samtools view -u -f 2048 in.bam)

This will output BAM to stdout, replace - with an actual output filename.

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written by dariober dariober

Maybe worth noting that this will output duplicate alignments if a record matches more than one OR conditions (e.g. for 2052 which is not really possible in this case but you never know...)

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written by dariober dariober

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