Data preparation

TOPMed Imputation Server accepts VCF files compressed with bgzip. Please make sure the following requirements are met:

  • Create a separate vcf.gz file for each chromosome.
  • Variants must be sorted by genomic position.
  • GRCh37 or GRCh38 coordinates are required.
  • If your input data is GRCh37/hg19, please ensure chromosomes are encoded without prefix (e.g. 20).
  • If your input data is GRCh38/hg38, please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20).
  • VCF files need to be version 4.2 (or lower). This is specified in the VCF file header section.
  • Must contain GT field in the FORMAT column. All other FORMAT fields will be ignored. (if you are seeing problems with very large uploads, it may help to remove other FORMAT fields)
  • Due to server resource requirements, there is a maximum of 25k samples per chromosome per job (and a minimum of 20 samples). Please see the FAQ for details.

Note

Multiple *.vcf.gz files (one per chromosome) can be uploaded as part of a single job.

Quality Control for HRC, 1000G and CAAPA imputation

Will Rayner provides a great toolbox to prepare data: HRC or 1000G Pre-imputation Checks.

The main steps for HRC are:

Download tool and sites

wget http://www.well.ox.ac.uk/~wrayner/tools/HRC-1000G-check-bim-v4.2.7.zip
wget ftp://ngs.sanger.ac.uk/production/hrc/HRC.r1-1/HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz

Convert ped/map to bed

plink --file <input-file> --make-bed --out <output-file>

Create a frequency file

plink --freq --bfile <input> --out <freq-file>

Execute script

perl HRC-1000G-check-bim.pl -b <bim file> -f <freq-file> -r HRC.r1-1.GRCh37.wgs.mac5.sites.tab -h
sh Run-plink.sh

Create vcf using VcfCooker

vcfCooker --in-bfile <bim file> --ref <reference.fasta>  --out <output-vcf> --write-vcf
bgzip <output-vcf>

Additional Tools

Convert ped/map files to VCF files

Several tools are available: plink2, BCFtools or VcfCooker. 

plink --ped study_chr1.ped --map study_chr1.map --export vcf-4.2 --recode vcf --out study_chr1

Create a sorted vcf.gz file using BCFtools:

bcftools sort study_chr1.vcf -Oz -o study_chr1.vcf.gz

CheckVCF

Use checkVCF to ensure that the VCF files are valid. checkVCF proposes "Action Items" (e.g. upload to sftp server), which can be ignored. Only the validity should be checked with this command.

checkVCF.py -r human_g1k_v37.fasta -o out mystudy_chr1.vcf.gz