Dear all,
I would like to extract from a BAM (or SAM) file the reads that contain a specified nucleotide at a specified location. E.g. I would like to extract all reads that have the reference allele (T) at chr1:222222.
All the tools that I could find around simply subset a BAM based on an input position, but I cannot find anything that is able to subset based on which base is at that position.
Any ideas on how this could be accomplished?
Thank a lot!
I would like to extract from a BAM (or SAM) file the reads that contain a specified nucleotide at a specified location. E.g. I would like to extract all reads that have the reference allele (T) at chr1:222222.
All the tools that I could find around simply subset a BAM based on an input position, but I cannot find anything that is able to subset based on which base is at that position.
Any ideas on how this could be accomplished?
Thank a lot!
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