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#3 Quality scores missing when run as a single sample
Hello,
I am running some samples with the "--single" mode and the VCF generated from Scalpel does not seem to have any Quality scores in it. Is there a feature I can play with or a way to add the quality scores for the variants in it.
I approcate your help
Thank you,
Ashini
Hi Ashini,
the quality score for a variant in single mode is availabe as CHI2 (chi-squared score) within the INFO field.
Great. thats perfect. Thank you for your reply.
Ashini
Hi Ashini,
As per our supplemental figure 4 from "Reducing INDEL calling errors in
whole genome and exome sequencing data
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0089-z",
the variant quality is a function of both chi-square score and alternative
allele coverage (how many reads were supporting the variant). So you might
want to consider both metrics when understanding the data.
[image: Inline image 1]
On a side note, we have a new protocol paper that described the use of
scalpel step by step. You are welcome to check it out. Thanks.
Indel variant analysis of short-read sequencing data with Scalpel
http://www.nature.com/nprot/journal/v11/n12/full/nprot.2016.150.html
Best,
Han
On Mon, Jan 23, 2017 at 11:16 AM, Ashini Bolia abolia@users.sf.net wrote:
--
Han Fang
PhD student, Simons Center for Quantitative Biology
Cold Spring Harbor Laboratory
PhD student, Applied Math & Statistics
Stony Brook University
Email: hanfang.cshl@gmail.com
Website: http://hanfang.github.io/
Related
Feature request: #3
Hi Han,
Thanks for the sharing the article. It will be pretty useful. We look at coverage counts but also wanted to see if we can get some sort of quality metrics as well. It now makes much more sense that we have both chi square score and coverage counts.
Thank you again for your help.
Ashini