samfile.pileup How to get reference base
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Dieter
Oct 10, 2011, 6:04:02 PM10/10/11
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I am getting started with pysam and I am using pileup to iterate over
the pileupcolumns, get the coverage and the bases in the reads. What
is not immediately clear to me is: How do I get the reference base?
Many thanks in advance.
the pileupcolumns, get the coverage and the bases in the reads. What
is not immediately clear to me is: How do I get the reference base?
Many thanks in advance.
Andreas
Oct 17, 2011, 4:00:02 AM10/17/11
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Hi Dieter,
the reference sequence is not part of a bam/sam file. Hence, it can
not
be got at via a Samfile object.
You will need the sequence and get the base via the position - you can
use pysam.Fastafile to access faidx indexed fasta
files, for example.
Best wishes,
Andreas
the reference sequence is not part of a bam/sam file. Hence, it can
not
be got at via a Samfile object.
You will need the sequence and get the base via the position - you can
use pysam.Fastafile to access faidx indexed fasta
files, for example.
Best wishes,
Andreas
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