I originally asked this question on the pysam mailing list but my experience has been that the developers are not supporting pysam through that mailing list (none of my questions were answered in the same day and some were not answered at all, and the documentation is not very detailed). I still like the idea of using pysam and if biostar proves to be a better platform for support I plan to continue using it.
Here is my question: If I wanted to call snps over a region of 100KB in chr16 can I use IteratorSNPCalls and specify a startposition and iterate from there or do I need to iterate over the whole file from start until the position I am interested? Thanks
my example per below answer: SNPCaller example:
pileup_iter = samfile.pileup (stepper = 'samtools' , fastafile=fastafile) snpcaller= pysam.SNPCaller(pileup_iter) sc= snpcaller.call('chr16',73310450)
pileup_iter = samfile.pileup ('chr16',73310450,73310460, stepper = 'samtools' , fastafile=fastafile) snpcall_iter= pysam.IteratorSNPCalls(pileup_iter) for call in snpcall_iter: print str(call)