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23andMe / yhaplo

Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men
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About the 1000 Genomes dataset #18

Closed Caiyong-Yin closed 3 years ago

Caiyong-Yin commented 3 years ago

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

dpoznik commented 3 years ago

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 commented 3 years ago

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.

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