Zp to bgz convertion

Hail Query & hailctl
1

Hi All,
I installed Hail in our sever and it works perfectly with the data provided for the tutorial.
But when I tired to load the the vcf files of 200kexomes of Biobank, hail fails.
The vcf files are in .zp ending but bgzip to file name did not work for me.
I tried $cat unzip myfile.zp| bgzip > myfile.bgz
It does not make a compressed file, seems simply changes the name.

I would be grateful if you can helpe with this.
Thank you
Reshmi

2

Hi Reshmi,

Thanks for reaching out. This sounds like issue with the Biobank data. Where did you download the files from?

Thanks,
Chris

3

It was downloaded by another group and shared with me.But I do see that they use plink and other tools to get GWAS done on the file and seems the files are fine. May I send you the error reports.

4

Posting the error you got from hail may be helpful