I am trying to "brute-force" split a bam file using grep. The reason why I am doing this is because I am trying to split by a custom tag that looks like these (bc would be the tag):
(( But I cannot used bamtools because "bc" is not a recognized tag )). My file is small-sih (<3 GB) so I used grep to make my split files and appended the header to each sub-file.
But something is wrong because I cannot index my new sub-files. I ran ValidateSamFile from picard, and it is pointing to a missing tag in the header ("Error parsing SAM header. @RG line missing SM tag.") but not the one that I am interested in.
Does anyone know what I am doing wrong ?