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Odd variant call quality distribution

BlueBlue Posts: 24Member

Basically I have an odd-looking distribution of my variant quality scores (see attached png), and was wondering how concerned should I be and how can I rectify it.

The input data from the graph is from UnifiedGenotyper vcf output file, QUAL values. The four samples in the vcf file are one Drosophila reference line, and three more which are outcrosses of the reference line and thus are heterozygous for the reference allele.

My fastq read-mapping pipeline includes adapter and low-quality base removal, and local re-alignment. I've also attached a pdf showing read quality distribution from one of the samples which also looks a bit odd.

qualscoredistr.png
1261 x 804 - 67K
pdf
pdf
TH1_CRSNR.multiplemetrics.quality_distribution.pdf
5K

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,418Administrator, GATK Developer admin

    Unfortunately we don't have the resources to provide detailed troubleshooting of your results, sorry. If you think the distributions look odd, perhaps you can look in more detail at subsets of variants from different tranches in IGV, to get an idea of whether they look real or not. You may need to play around with parameters of variant recalibration to find the settings that suit your data best. Good luck!

    Geraldine Van der Auwera, PhD

  • BlueBlue Posts: 24Member

    This QUAL distribution anomaly exists at a similar level in all chromosomes. I'm not performing variant recalibration because most of the variants are likely to be novel.

    In the UnifiedGenotyper, what metrics go into the calculation which generates the QUAL value for each variant ?

    I cannot see this information in the documentation.

    I assume that total depth, 'DP' is one of them.

    My DP distribution is normal so there must be something else affecting my QUAL.

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