TY - JOUR
T1 - VariantQC
T2 - A visual quality control report for variant evaluation
AU - Yan, Melissa Y.
AU - Ferguson, Betsy
AU - Bimber, Benjamin N.
N1 - Publisher Copyright:
© 2019 The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
PY - 2019/12/15
Y1 - 2019/12/15
N2 - Large scale genomic studies produce millions of sequence variants, generating datasets far too massive for manual inspection. To ensure variant and genotype data are consistent and accurate, it is necessary to evaluate variants prior to downstream analysis using quality control (QC) reports. Variant call format (VCF) files are the standard format for representing variant data; however, generating summary statistics from these files is not always straightforward. While tools to summarize variant data exist, they generally produce simple text file tables, which still require additional processing and interpretation. VariantQC fills this gap as a user friendly, interactive visual QC report that generates and concisely summarizes statistics from VCF files. The report aggregates and summarizes variants by dataset, chromosome, sample and filter type. The VariantQC report is useful for high-level dataset summary, quality control and helps flag outliers. Furthermore, VariantQC operates on VCF files, so it can be easily integrated into many existing variant pipelines.
AB - Large scale genomic studies produce millions of sequence variants, generating datasets far too massive for manual inspection. To ensure variant and genotype data are consistent and accurate, it is necessary to evaluate variants prior to downstream analysis using quality control (QC) reports. Variant call format (VCF) files are the standard format for representing variant data; however, generating summary statistics from these files is not always straightforward. While tools to summarize variant data exist, they generally produce simple text file tables, which still require additional processing and interpretation. VariantQC fills this gap as a user friendly, interactive visual QC report that generates and concisely summarizes statistics from VCF files. The report aggregates and summarizes variants by dataset, chromosome, sample and filter type. The VariantQC report is useful for high-level dataset summary, quality control and helps flag outliers. Furthermore, VariantQC operates on VCF files, so it can be easily integrated into many existing variant pipelines.
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U2 - 10.1093/bioinformatics/btz560
DO - 10.1093/bioinformatics/btz560
M3 - Article
C2 - 31309221
AN - SCOPUS:85077776916
SN - 1367-4803
VL - 35
SP - 5370
EP - 5371
JO - Bioinformatics
JF - Bioinformatics
IS - 24
ER -