Extract reads from bam files by their @RG

Question

How could I extract reads from bam files by their read groups @RG ?, I've got one file containing all reads for 5 samples, the SM is appears NONE, So, I want to extract each sample reads by the @RG tags.

Answer 1

Typically I use samtools for operations like this. Specifically I use samtools view with either -r or -R flag depending on the use case.

-r STR
Output alignments in read group STR [null]. Note that records with no RG tag will also be output when using this option. This behaviour may change in a future release.

-R FILE
Output alignments in read groups listed in FILE [null]. Note that records with no RG tag will also be output when using this option. This behaviour may change in a future release.

Answer 2

This sounds more like a job for samtools split if you want to split out all the read groups into separate bams in one go.

http://www.htslib.org/doc/samtools-split.html

samtools split [options] merged.sam|merged.bam|merged.cram

Splits a file by read group.

Options:

-u FILE1
Put reads with no RG tag or an unrecognised RG tag into FILE1

-u FILE1:FILE2
As above, but assigns an RG tag as given in the header of FILE2

-f STRING
Output filename format string (see below) ["%*_%#.%."]

-v
Verbose output

Alternatively if you do want to proceed one read group at a time, in addition to samtools view, you can also do this with GATK using the PrintReads tool with the ReadGroupReadFilter as documented here:

https://gatk.broadinstitute.org/hc/en-us/articles/360041415172-ReadGroupReadFilter

The command line would look like this:

gatk PrintReads \
   -I input.bam \
   --read-filter ReadGroupReadFilter \
   --keep-read-group <RG:readgroup> \
   -O output.bam

There's also a filter called ReadGroupBlackListReadFilter that allows you to exclude a list of readgroups.

https://gatk.broadinstitute.org/hc/en-us/articles/360041851151-ReadGroupBlackListReadFilter

The PrintReads tool doc is here:

https://gatk.broadinstitute.org/hc/en-us/articles/360041849911-PrintReads