reads name for alt base pysam
need to get read names that have alt ref from a bamfile
so far i was able to write this but i am not sure what syntax to use after my for loop to query:
ref= 'T'
alt = 'C'
samfile= pysam.Samfile('bamfile', 'rb')
for pileupcolumn in samfile.pileup("2", start -1 , end):
for pileupread in pileupcolumn.pileups:
pileupread.alt_base?
Could some one help me with syntax thanks
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What do you mean by "alt ref"?