Extracting percent identity of mapped reads and the coordinates on the genome the read mapped from a BAM file?
Hello,
I am working with bam files that have environmental reads mapped back to an isolate genome. I am looking for a way to extract both the percent identity of all mapped reads in the BAM file and the coordinates on the genome where they mapped. I was looking at some combination of maybe bedtools and pysam or parsing the CIGAR string but nothing I have tried has worked so far.
I was trying to find a pythonic answer, but if people have other solutions feel free to share.
Thanks!
1 answer
If you use pysam:
samfile = pysam.AlignmentFile("your_bam", "rb")
for read in samfile.fetch():
cig=read.cigarstring #for cigarstring
aligned=read.get_aligned_pairs() # will give you the aligned pairs
Be careful 'M' in cigar also include SNPs
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