Hi everyone,
I have a BAM file containing aligned reads to a reference. I need to calculate a consensus sequence but not from all the reads in the BAM file but only from a subset, and I know in advance which sequences I am interested in.
Is there a tool that would allow me to do this task?
I think I can extract the required sequences from the BAM file and map them to a reference myself. I would like to avoid that (re-mapping part) because the reads in the original BAM file were already aligned based on specific criteria and I want to keep that alignment.
Thanks.
I have a BAM file containing aligned reads to a reference. I need to calculate a consensus sequence but not from all the reads in the BAM file but only from a subset, and I know in advance which sequences I am interested in.
Is there a tool that would allow me to do this task?
I think I can extract the required sequences from the BAM file and map them to a reference myself. I would like to avoid that (re-mapping part) because the reads in the original BAM file were already aligned based on specific criteria and I want to keep that alignment.
Thanks.
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