Greetings all, The problem before me is as follows:
I have a pretty large .bam file, and from that file I need to find all mapping locations of a particular read name ("
queryname" according to
.bam lingo). Is there any way to do so efficiently?
picard offers "
FilterSamReads.jar", but this method is actually even slower than converting the
.bam file to a
.sam file and just using
grep to extract reads with specific names.
In particular, one would imagine that one could take advantage of sorting the
.bam file by
samtools sort -n) to do this efficiently in a similar manner to which one can extract all mappings to a particular reference in coordinate-sorted
.bam files (produced by "
samtools sort" within the
So, the main purpose of writing this is to verify that no efficient method actually exists before spending the time writing a new one.