Twelve years of SAMtools and BCFtools
P Danecek, JK Bonfield, J Liddle, J Marshall… - …, 2021 - academic.oup.com
Background SAMtools and BCFtools are widely used programs for processing and analysing
high-throughput sequencing data. They include tools for file format conversion and …
high-throughput sequencing data. They include tools for file format conversion and …
The variant call format and VCFtools
The variant call format (VCF) is a generic format for storing DNA polymorphism data such as
SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is …
SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is …
[HTML][HTML] Mouse genomic variation and its effect on phenotypes and gene regulation
We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten
times more variants than previously known. We use these genomes to explore the …
times more variants than previously known. We use these genomes to explore the …
Reference-based phasing using the Haplotype Reference Consortium panel
… All differences were significant (binomial P ≤ 0.003 for each comparison of Eagle2 with
SHAPEIT2, P ≤ 0.02 for each comparison with Eagle1, and P = 10 −21 for each comparison …
SHAPEIT2, P ≤ 0.02 for each comparison with Eagle1, and P = 10 −21 for each comparison …
Evidence for 28 genetic disorders discovered by combining healthcare and research data
… P values from analysis of the undiagnosed subset for discordant and novel genes; P values
for consensus genes come from the full cohort analysis. The number of genes in each P-…
for consensus genes come from the full cohort analysis. The number of genes in each P-…
Whole‐genome sequencing identifies EN1 as a determinant of bone density and fracture
The extent to which low‐frequency (minor allele frequency (MAF) between 1–5%) and rare (MAF
≤ 1%) variants contribute to complex traits and disease in the general population is …
≤ 1%) variants contribute to complex traits and disease in the general population is …
Common genetic variation drives molecular heterogeneity in human iPSCs
…, D Bensaddek, FP Casale, OJ Culley, P Danecek… - Nature, 2017 - nature.com
… This was defined as the number of control variant sets (n) that showed a higher overlap with
the target annotation than the eQTL lead variants (P = n / 100). The empirical P values were …
the target annotation than the eQTL lead variants (P = n / 100). The empirical P values were …
Insights into human genetic variation and population history from 929 diverse genomes
INTRODUCTION Large-scale human genome-sequencing studies to date have been limited
to large, metropolitan populations or to small numbers of genomes from each group. Much …
to large, metropolitan populations or to small numbers of genomes from each group. Much …
EIDA: The European integrated data archive and service infrastructure within ORFEUS
The European Integrated Data Archive (EIDA) is the infrastructure that provides access to
the seismic‐waveform archives collected by European agencies. This distributed system is …
the seismic‐waveform archives collected by European agencies. This distributed system is …
[HTML][HTML] A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains
…, H Cater, MF Champy, R Combe, P Danecek… - Genome biology, 2013 - Springer
Background The mouse inbred line C57BL/6J is widely used in mouse genetics and its
genome has been incorporated into many genetic reference populations. More recently large …
genome has been incorporated into many genetic reference populations. More recently large …