Identify reads aligned to mutant and wild type sequences
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rpauly commented
Hi,
Is there a way to identify the number of reads that aligned to the mutant and wild type sequences using bam-readcounts?
Thanks!
chrisamiller commented
Yes, assuming that you know the location of informative sites in the genome, querying that position with bam-readcount will return the counts of each base at that location and allow you to count wild type or mutant reads.