WES variant calling with DNBSEQ-T7 - technical quality assessment

Question

[bompipi95]

Hi everyone!

I recently received whole exome sequencing samples that were sequenced on an MGI sequencing instrument, DNBSEQ-T7. I am interested in somatic variant-calling on the paired tumor-normal samples. As this isn't the canonical Illumina sequencer, an issue that I am concerned with is that the technical artefacts arising from the sequencer is not yet well characterised and this may lead to spurious artefacts in the variants.

I asked the company that did the sequencing for a panel of normals (PON) for the instrument to run Mutect2, but they simply replied that they use the standard GATK PON for their somatic variant calls.

How should I go about assessing whether the variants are "biased" in any way, as a result of the instrument's technical properties? Is there a way to quantify the magnitude of these technical errors from the VCF files?

Answer 1

[colindaven]

This is a complex topic and is best answered by studying the methods sections of comparison papers.

This is an excellent preprint from 2020 which likely got published in a high impact journal by the Mason lab which compares multiple sequencers.

https://www.biorxiv.org/content/10.1101/2020.07.23.218602v1.full

From what I have seen, the MGI sequencers are on par or better than Illumina for accuracy - but that said, most of our own comparisons were vs the outdated Illumina Nextseq550, which has quite substandard quality in the 150bp read option, though 75bp reads were good quality.

You should probably run the data through fastqc, fastp and other tools to check quality, then also use multiqc for a summary.