Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comment
. 2020 Nov 1;36(17):4671-4672.
doi: 10.1093/bioinformatics/btaa514.

Reference bias in the Illumina Isaac aligner

Alex J Cornish  1 , Daniel Chubb  1 , Anna Frangou  2   3 , Phuc H Hoang  1 , Martin Kaiser  4 , David C Wedge  2   3   5 , Richard S Houlston  1
Affiliations
Comment

Reference bias in the Illumina Isaac aligner

Alex J Cornish et al. Bioinformatics. .
No abstract available

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Evidence of reference bias from Isaac. (A) Heterozygous SNP VAF distributions in sequencing data from 25 normal samples. Dashed line represents expected median VAF of 0.5. Whiskers extend 1.5 times inter-quartile range and values outside of this range are not shown. (B) Proportion of reads covering SNP positions supporting the reference (blue line) and alternate (red line) alleles with that read position soft clipped. (C) SNV VAFs from 25 tumor-normal pairs. (D) CCFs of clonal mutation clusters identified by DPClust. Blue and grey dashed lines denote the median putative clonal mutation cluster CCF and a CCF of 1, respectively. (E) Ccube sample purity estimates. Distribution differences assessed using Wilcoxon Signed-Rank test
See this image and copyright information in PMC

Comment on

References

    1. Burns A. et al. (2018) Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHV(mut) and IgHV(unmut) subgroups. Leukemia, 32, 332–342. - PMC - PubMed
    1. Dentro S.C. et al. (2017) Principles of reconstructing the subclonal architecture of cancers. Cold Spring Harb. Perspect. Med., 7, a026625. - PMC - PubMed
    1. Kim S. et al. (2018) Strelka2: fast and accurate calling of germline and somatic variants. Nat. Methods, 15, 591–594. - PubMed
    1. Li H., Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760. - PMC - PubMed
    1. Nik-Zainal S. et al. (2012) The life history of 21 breast cancers. Cell, 149, 994–1007. - PMC - PubMed