Python script to find error rate
I am trying to write a python script that, from a BAM files, calculates the error rate of the DNA sequencing based on the reference genome. I am brand new to bioinformatics, and I am very stuck. This is what I have so far:
import pysam
samfile = pysam.AlignmentFile("TruQ3_229.sorted.bam", "rb")
for pileupcolumn in samfile.pileup("chr1", 100, 120)
I have no idea what to do and where to continue. Any help is appreciated. Thanks!
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What is your definition of error rate? Have you first tried summarizing what do you want to achieve? While posting a question, please try to provide as much as information as possible.
Hi zaidnab,
While not a full answer, you can find some ideas in my recent blog post: Getting the edit distance from a bam alignment: a journey. Let me know if you need further help.
I see you started to make pileups, but I believe you want a per-read error rate?