Hi im looking for the aligned bases in the reads for a given reference position. im using the following script from the pysam documentataion. I adjusted it to find the specified position. in this case 24793.
import pysam samfile = pysam.AlignmentFile("generated_alignment_sorted.bam", "rb" ) for pileupcolumn in samfile.pileup("chr05_modified.copy0", 10, 52000000): if pileupcolumn.pos == 24793: print ("\ncoverage at base %s = %s" % (pileupcolumn.pos, pileupcolumn.n)) for pileupread in pileupcolumn.pileups: print ('\tbase in read %s = %s' % (pileupread.alignment.query_name.split(';'), pileupread.alignment.query_sequence[pileupread.query_position])) samfile.close()
coverage at base 24793 = 6 base in read m419941/6207/CCS Read=419941 = C
For all the position I tried it doesnt print out the same number of bases as it says that the coverage is. shouldnt this print out 6 times: base in read m419941/6207/CCS Read=419941 = C for different reads?
Why is this?