Hi All,

I want to know if there is a way to extract variant nucleotide(s) from
reads
that align to particular locations. This should also take care of the
soft/hard clips, split alignments etc.
I have a filtered BAM file with reads which cover my loci of interest.  For
example an an insertion GAA
exists in the reference at ch1:1234-1236. I want to tabulate all variant
alleles at ch1:1234-1236.

Thanks,
Alpesh

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