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Trying to call SNPs #136

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi,

I see that the SNPCaller Class has been removed from the latest versions of 
pysam. How do you I get SNP information - like variant coverage, variant allele 
frequency etc using pysam?

Thanks,
RS

Original issue reported on code.google.com by rohini.1...@gmail.com on 13 Sep 2013 at 9:14

GoogleCodeExporter commented 9 years ago 
Hi RS,

the best way is to use the pysam.mpileup command and parse the output
directly.

SNP calling is highly complex and heavily parameterized. There was a danger
that the pysam implementations might show different behaviour from the samtools
implementation, which would have caused a lot of confusion.

I have added some text to the documentation.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 17 Sep 2013 at 7:24