samtag is a command-line tool for tagging reads in a BAM/CRAM file whose name appear in an input list. It is possible to specify default a tag/flag applied to every read and/or per-read tags/flags. samtag can also generate statistics about tags and their values based on regular expressions.
The minimal input is a BAM/CRAM file and a TSV specifying read names in the first column, a tag in the second column (optional), and flags in the third column (optional). The format for tags is TAG:VALUE, unless a default tag is provided with the --tag option without a value, in which case the TAG names in the input file can be ommitted (i.e. just specify VALUE).
# Add "ZA:Z:FOO" tag to all reads in test/reads1.tsv,
# in addition to tags/flags specified in test/reads1.tsv.
$ samtag tag --tag ZA:BAR -o tagged1.bam test/test.bam test/reads1.tsv
# Add "ZA" tag to all reads in test/reads2.tsv,
# with the values specified in test/reads2.tsv.
$ samtag tag --tag ZA -o tagged2.bam test/test.bam test/reads2.tsvTo compute statistics about tags:
$ samtag stats --tag ZA tagged1.bam
tag value count fraction
* * 3859 1
ZA * 8 0.00207308
$ samtag stats --tag ZA --split --sort tagged1.bam
tag value count fraction
* * 3859 1
ZA * 8 0.00207308
ZA BAR 7 0.00181394
ZA FOO 1 0.000259134
$ samtag stats --tag ZA:BAR tagged1.bam
tag value count fraction
* * 3859 1
ZA BAR 7 0.00181394
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