Skip to content

Instantly share code, notes, and snippets.

@hardingnj

hardingnj/shapeit_bug_report

Last active August 29, 2015 14:08
Show Gist options
  • Save hardingnj/6945219038457e6c1cb9 to your computer and use it in GitHub Desktop.
Save hardingnj/6945219038457e6c1cb9 to your computer and use it in GitHub Desktop.
Download ZIP
Bash script to highlight potential bug in shapeIt
Raw
shapeit_bug_report
#! /bin/bash
curl -O https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/files/example.tar.gz
tar -xvzf example.tar.gz
FILE=example/GLs.vcf
gunzip ${FILE}.gz
shapeit --input-vcf $FILE --output-max unzipped.haps unzipped.sample
gzip -c ${FILE} > ${FILE}.gzip.vcf.gz
shapeit --input-vcf ${FILE}.gzip.vcf.gz --output-max gzipped.haps gzipped.sample
bgzip -c ${FILE} > ${FILE}.bgzip.vcf.gz
shapeit --input-vcf ${FILE}.bgzip.vcf.gz --output-max bgzipped.haps bgzipped.sample
tail -n 1 *haps | less -S
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment