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Bioawk: multiple criteria

From the example:

awk -c sam 'and($flag,4)' aln.sam.gz

How can I add and($flag,64) as another criterion? None of the various syntaxes I tried works.

Thanks

bioawk
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updated by Ram Ram • written by bongbang • bongbang

2 answers

Simply add the numbers and use it. In your case use 64+4=68. The command you mentioned will extract unmapped reads ($flag,4) and if you use ($flag,68), then it will extract unmapped reads that are first in pair. I have never used bioawk for this purpose but this is my guess.

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updated by Ram Ram • written by Ashutosh Pandey Ashutosh Pandey

That really should work, but it doesn't.

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written by bongbang • bongbang

It would be really surprising if this did not work. Then why would the original and($flag, 4) work?

I ran a test and the results look as expected:

$ samtools view -c -F 68 bam/SRR1553595.bam 
1027
$ samtools view bam/SRR1553595.bam | bioawk -c sam ' !and($flag, 68)' | wc -l
1027

Edit: actually I get a different result in this case:

$ samtools view -c -f 68 bam/SRR1553595.bam 
19083
$ samtools view bam/SRR1553595.bam | bioawk -c sam ' and($flag, 68)' | wc -l
39050
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updated by Ram Ram • written by Istvan Albert Istvan Albert

This should work as well:

bioawk -c sam 'and($flag, 4) && and($flag, 64)'
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updated by Ram Ram • written by dariober dariober

That does work (Thank you!), but see my answer for a more idiomatic syntax.

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written by bongbang • bongbang

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