About the 1000 Genomes dataset

Question

About the 1000 Genomes dataset

Caiyong-Yin opened this issue 4 years ago · comments

Dear authors,

When I hanle the 1000 Genomes dataset by the code 'yhaplo -i 1000y.all.vcf.gz', the linux system responds that ‘ERROR. Could not open: 1000Y.all.vcf.gz’. I have check the path and the name of the data. So how could I solve this problem?

Caiyong Yin
Fudan University

David Poznik · Answer 1 · Thu Oct 22 2020 01:58:00 GMT+0800 (China Standard Time)

Hmm, I just downloaded a fresh copy of the file from:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/chrY/ALL.chrY_10Mbp_mask.glia_freebayes_maxLikGT_siteQC.20130502.60555_biallelic_snps.vcf.gz

I then ran:

ln -sf ALL.chrY_10Mbp_mask.glia_freebayes_maxLikGT_siteQC.20130502.60555_biallelic_snps.vcf.gz 1000y.all.vcf.gz
yhaplo -i 1000y.all.vcf.gz

And it worked fine. So I'm guessing your download was corrupted. You could try reading the file with tabix:

tabix -p vcf 1000y.all.vcf.gz
tabix -H 1000y.all.vcf.gz

But it's probably easiest to just re-download.

Caiyong-Yin · Answer 2 · Thu Oct 22 2020 17:21:36 GMT+0800 (China Standard Time)

Thanks. My issue has been solved following your suggestions. cyyin18 邮箱：cyyin18@fudan.edu.cn On 10/22/2020 01:58, David Poznik wrote: Hmm, I just downloaded a fresh copy of the file from: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/chrY/ALL.chrY_10Mbp_mask.glia_freebayes_maxLikGT_siteQC.20130502.60555_biallelic_snps.vcf.gz I then ran: ln -sf ALL.chrY_10Mbp_mask.glia_freebayes_maxLikGT_siteQC.20130502.60555_biallelic_snps.vcf.gz 1000y.all.vcf.gz yhaplo -i 1000y.all.vcf.gz And it worked fine. So I'm guessing your download was corrupted. You could try reading the file with tabix: tabix -p vcf 1000y.all.vcf.gz tabix -H 1000y.all.vcf.gz But it's probably easiest to just re-download. —You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe. [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "#18 (comment)", "url": "#18 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]