I've got GWAS data in plink format (.fam, .bed, .bim). I want to impute snps that weren't directly sequenced. I've read that IMPUTE2 is good. I gather I need to phase the data before. I've read SHAPEIT is good for that. I've downloaded it from here https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download I untar it with
tar -zxvf shapeit.v2.r904.glibcv2.17.linux.tar.gz
the folder shapeit.v2.904.3.10.0-693.11.6.el7.x86_64 contains: LICENCE, bin, example The executable looks to be in bin. As per instructions, I try to run the example from the shapeit.v2.904.3.10.0-693.11.6.el7.x86_64 folder, or from bin, or from example folder:
shapeit --input-bed gwas.bed gwas.bim gwas.fam \
--input-map genetic_map.txt \
--output-max gwas.phased.haps gwas.phased.sample
But all I get is:
zsh: exec format error: shapeit
Can anyone help?
what is the architecture of your computer ? you downloaded a 64 bit software. It'll fail if you're computer is a 32 bit.
Have you added the path to shapeit to your environment variable? If not, you should use /path/to/your/shapeit instead of shapeit to run the command
I think the issue may be I have a mac running Catalina. Is there a way to run shapeit on mac??
If
shapeitis a 32-bit app then you are out of luck running natively. You can use a VM on catalina.It’s 64 bit I believe. Can anyone help me run it on a Mac?
https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
Even though macOS is BSD-unix based it is not directly equivalent to linux. Unfortunately it appears that only linux binaries are available for
shapeitsoftware from the link you posted. These will not work on macOS catalina or older versions as is. If this is only hardware you have access to you may need to install a virtual machine running linux to be able to run this program.