I am trying to use bamtools filter to keep output a new bam file with a specific sequence. This is what I am using...
bamtools filter -in Aligned.bam -queryBases AAACCTG >Aligned_1.bam
This does not return any matches. The question I am asking, is it possible to filter sequencing reads from a BAM file that has specific sequence of interest? If so, how? Are there any other tools that might be able to do this?
Thanks in advance for any guidance provided.