Hi there,
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):
bc:B:S,1,1
bc:B:S,0,0
bc:B:S,2,2
(( 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 ?
2 answers
ran ValidateSamFile from picard, and it is pointing to a missing tag in the header ("Error parsing SAM header. @RG line missing SM tag."
that because you're ignoring the bam header
use
samtools view -h in.bam | grep -E '(^@|bc\:B\:S,1,1)' | samtools view -S -b -o out.bam -
EDIT: when using ValidateSamFile you must also specify what should(not) be checked: http://broadinstitute.github.io/picard/command-line-overview.html#ValidateSamFile
e.g:
IGNORE=RECORD_MISSING_READ_GROUP
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