Sanger Imputation Service protocols

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Sanger Imputation Service specifications

Information


Unique identifier OMICS_17678
Name Sanger Imputation Service
Interface Web user interface
Restrictions to use None
Input format VCF, 23andMe
Output data Phasing-only pipeline, imputation pipelines, a tarball of the various log files associated with the pipeline.
Output format VCF
Computer skills Basic
Stability Beta
Maintained Yes

Documentation


Additional information


https://imputation.sanger.ac.uk/?instructions=1#prepareyourdata; A registration is needed to access to tools.

Publication for Sanger Imputation Service

Sanger Imputation Service in pipelines

 (2)
2017
PMCID: 5600256
PMID: 28604731
DOI: 10.1038/ng.3888

[…] were genotyped using the affymetrix axiom ceu array and the axiom gt1 algorithm. genome-wide imputation of autosomal snps according to phase 3 of the 1000 genomes project was performed at the sanger imputation service (see ). quality control before imputation removed variants with genotyping rate of less than 95%, minor allele frequency of less than 10 × 10-3, or strong deviation […]

2017
PMCID: 5600256
PMID: 28604731
DOI: 10.1038/ng.3888

[…] genotyping and qc, http://biobank.ctsu.ox.ac.uk/crystal/refer.cgi?id=155580; snptest, https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html; magma, http://ctg.cncr.nl/software/magma; sanger imputation service, https://imputation.sanger.ac.uk/; genotyping chip strand files, www.well.ox.ac.uk/~wrayner/strand/; dbsnp data, ftp://ftp.ncbi.nih.gov/snp/; plink, […]

Sanger Imputation Service in publications

 (4)
PMCID: 5519631
PMID: 28729679
DOI: 10.1038/s41598-017-05445-3

[…] 3) 1000 genomes project (1000g) reference panel alone, and 3) a merged panel comprising both the agrp and the 1000g reference panel., we also uploaded the phased vcf file of the test set to the sanger imputation service (https://imputation.sanger.ac.uk/) and imputed the masked sites with the pbwt pipeline against the haplotype reference consortium (r1.1) reference panel. variant sites […]

PMCID: 5600256
PMID: 28604731
DOI: 10.1038/ng.3888

[…] were genotyped using the affymetrix axiom ceu array and the axiom gt1 algorithm. genome-wide imputation of autosomal snps according to phase 3 of the 1000 genomes project was performed at the sanger imputation service (see ). quality control before imputation removed variants with genotyping rate of less than 95%, minor allele frequency of less than 10 × 10-3, or strong deviation […]

PMCID: 5339960
PMID: 28270201
DOI: 10.1186/s13073-017-0414-4

[…] 2443 first cousins and 6599 avuncular (niece/nephew–aunt/uncle) relationships., in order to increase the density of variants throughout the genome, the genotyped data were imputed utilising the sanger imputation service [] using the hrc panel v1.1 [, ]. this exome sequence data will have greatly improved imputation quality across the whole cohort. autosomal haplotypes were checked to ensure […]

PMCID: 5671666
PMID: 29109912
DOI: 10.7717/peerj.3951

[…] sample. after these qc steps, we retained 377 samples and 520,076 markers., after performing the qc steps described above, the samples were phased using the program shapeit2 and imputed at the sanger imputation service, using the positional burrows-wheeler transform (pbwt) algorithm (), and the samples of the 1000 genomes as reference haplotypes., we used the program eigensoft to perform […]

Sanger Imputation Service institution(s)
Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; (etc.)
Sanger Imputation Service funding source(s)
Supported by the ERC (Grant no. 617306), the Wellcome Trust (Grant no. WT097307), Wellcome Trust grant WT098051.

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