NAME
fromsam
USAGE
Usage: recs fromsam <args> [<files>]
Each line of input (or lines of <files>) is parsed as a SAM (Sequence
Alignment/Map) formatted record to produce a recs output record. To parse a
BAM file, please pipe it from `samtools view file.bam` into this command.
The output records will contain the following fields:
qname flag rname pos mapq cigar rnext pnext tlen seq qual
Additional optional SAM fields are parsed into the "tag" key, which is a hash
keyed by the SAM field tag name. The values are also hashes containing a
"type" and "value" field. For example, a read group tag will end up in your
record like this:
tags => {
RG => {
type => "Z",
value => "...",
}
}
Refer to the SAM spec for field details: http://samtools.github.io/hts-
specs/SAMv1.pdf
Arguments:
--flags Decode flag bitstring into a "flags" hashref
--quals Decode qual string into a "quals" array of
numeric values
--filename-key|fk <keyspec> Add a key with the source filename (if no
filename is applicable will put NONE)
Help Options:
--help This help screen
Examples:
Parse SAM and calculate average mapping quality:
recs fromsam input.sam | recs collate -a avg,mapq
Parse BAM:
samtools view input.bam | recs fromsam
Parse SAM pre-filtered by read group:
samtools view -r SAMPLE-1234 input.sam | recs fromsam
The same, but probably slower:
recs fromsam input.sam | recs grep '{{tag/RG/value}} eq "SAMPLE-1234"'