How are expected error rates calculated?
0
0
Entering edit mode
6.4 years ago
Andrew ▴ 60

I want to find the overall expected error rate of reads in a BAM file, as well as the expected number of errors.

Currently for each base in a read, I find the ASCII value (number) of the quality (column 11), subtract 33, and remove the phred scale, which to my understanding would give me the probability that the base is wrong. I do this for every base in every read and sum the values up, and divide it by the total number of bases for all reads.

Is this correct? If not how would I calculate the expected error rate?

expected error rate BAM • 3.5k views
ADD COMMENT
1
Entering edit mode

That's correct, although note that a bam file can have multiple alignments for each read.

ADD REPLY
0
Entering edit mode

Hi Andrew, If it possible that you supply the command line that you use for this?

Also, other option to estimated per base error rate could be using mpileup file from the BAM file and then access to the data using command line tools like grep, cut, sed, awk, etc.

Thanks!

ADD REPLY

Login before adding your answer.

Traffic: 1429 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6