Hi @ll,
I want to do the following and have not found any suggestions on the web yet:
I would like to extract reads from a bam file that contain a certain mismatch to the reference.
This means irrespective of the remaining sequence, if a read contains for example a "G" instead of the reference allele "A" at any position I would like to write it into a separate bam file.
Do you think that is possible?
I do not want to call SNPs or get the number of non-ref bases in a region. I really want to extract the entire read with at least one specific mismatch (e.g. only A->G), no matter if there is a SNP at that position or not.
Thanks for you attention,
Seb
I want to do the following and have not found any suggestions on the web yet:
I would like to extract reads from a bam file that contain a certain mismatch to the reference.
This means irrespective of the remaining sequence, if a read contains for example a "G" instead of the reference allele "A" at any position I would like to write it into a separate bam file.
Do you think that is possible?
I do not want to call SNPs or get the number of non-ref bases in a region. I really want to extract the entire read with at least one specific mismatch (e.g. only A->G), no matter if there is a SNP at that position or not.
Thanks for you attention,
Seb
Comment