tabix

Web: https://github.com/samtools/htslib.

Their availability on CSD3 can be seen with

module avail tabix
module avail htslib
 

Its utility to extract data has only been realised recently

tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/BLUEPRINT/ge/BLUEPRINT_ge_monocyte.all.tsv.gz 20:46120612-46120613
tabix https://gwas.mrcieu.ac.uk/files/ebi-a-GCST010776/ebi-a-GCST010776.vcf.gz 1:1-1000000
 

with earlier versions possibly giving error messages; we install the latest,

module load gcc/6
wget -qO- https://github.com/samtools/htslib/releases/download/1.12/htslib-1.12.tar.bz2 | \
tar -vxjf -
cd htslib-1.12/
autoreconf -i
./configure --enable-libcurl --prefix=${HPC_WORK}
make
make install
 

One could obtain a list of outcomes as follows,

Rscript -e "write.table(TwoSampleMR::available_outcomes(),file='ao.txt',quote=FALSE,row.names=FALSE,sep='\t')"
 

NOTE

It also works with VCF files, e.g.,

tabix -p vcf TSLP.vcf.gz -h 1:100-100000

where the -h option is used to preserve the header information.

See specific section on bcftools for additional information.

bcftools query works similarly on a local VCF file nevertheless the option -r is necessary.

bcftools query -f '%ID\t%ALT\t%REF\t%AF\t[%ES]\t[%SE]\t[%LP]\t[%SS]\t%CHROM\t%POS\n' -r 1:1-1000000 \
               https://gwas.mrcieu.ac.uk/files/ebi-a-GCST010776/ebi-a-GCST010776.vcf.gz
 

The rather perplexing syntax (cut and paste from here in which case) gains its appeal for an output in a well-defined format.

Applications: Heart-KP

Web

http://heartkp.org/

Zenodo

#!/usr/bin/bash

wget https://zenodo.org/record/7239166/files/Bai82_names_ukb_v2.csv
seq 1 82 | \
parallel -j10 -C' ' '
  echo {}
  wget -qO- https://zenodo.org/record/7239166/files/ukbiobank_heart_pheno{}_may2022.zip | \
  gunzip -c | bgzip -f  > ukbiobank_heart_pheno{}_may2022.gz
  tabix -f -S1 -s1 -b3 -e3 ukbiobank_heart_pheno{}_may2022.gz
'
 

Reference

Zhao, B., T. Li, Z. Fan, Y. Yang, J. Shu, X. Yang, X. Wang, T. Luo, J. Tang, D. Xiong, Z. Wu, B. Li, J. Chen, Y. Shan, C. Tomlinson, Z. Zhu, Y. Li, J. L. Stein and H. Zhu "Heart-brain connections: Phenotypic and genetic insights from magnetic resonance images." Science 380(6648): abn6598. https://doi.org/10.1126/science.abn6598