Can Gatk Base Quality Recalibration Be Used With Amplicon Sequencing?
1
2
Entering edit mode
13.6 years ago
Casbon ★ 3.3k

GATK can recalibrate the quality scores in a sequencing run. However, would amplicon sequencing produce a rich enough data set to train the recalibrater.

For example, pretend I have one amplicon in my sequencing run with a novel SNP at a given position. This position would presumably get marked as low quality (since all the reads disagree with the reference). This means that trying to call SNPs from recalibrated scores would produce incorrect qualities, especially at variant sites?

snp gatk • 5.0k views
ADD COMMENT
3
Entering edit mode
13.6 years ago
Casbon ★ 3.3k

RTFM:

A critical determinant of the quality of the recalibation is the number of observed bases and mismatches in each bin. The system will not work well on a small number of aligned reads. We usually expect well in excess of 100M bases from a next-generation DNA sequencer per read group. 1B bases yields significantly better results.

Looks like recalibrating amplicon sequencing would be wrong, especially if using low numbers of pooled amplicons.

ADD COMMENT
0
Entering edit mode

Thanks for following up on this once you figured it out.

ADD REPLY
0
Entering edit mode

It may not be as bad as it seems if you have a few amplicons you could turn off the DiNucleotide covariates.

ADD REPLY

Login before adding your answer.

Traffic: 1260 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