1000 Genomes - Sample Subset Of A Vcf File
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11.9 years ago
pablo.riesgo ▴ 140

Hi there,

I'm trying to retrieve genotype data for a given sample from the 1000 genomes FTP repository, following their guidelines: http://www.1000genomes.org/faq/how-do-i-get-sub-section-vcf-file

So I tried to execute something like: tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz 1 | perl /nfs/1000g-work/G1K/work/bin/vcftools/perl/vcf-subset -c NA12890

This command is giving me an error at vcf-subset like: Wrong number of fields; expected 1101, got 559. The offending line was: [...]

At first sight you may think that it has got to do with the remote VCF file, but the line where it fails is different every execution and looks like it is cutting these lines. Anybody has the same problem?

Seems to me like a problem with tabix maybe cutting the lines when network is not working very well, but it is just a guess... Any other ideas?

Regards, Pablo.

PS: I'm gonna try downloading this huge files but I did not want to do this...

1000genomes vcf • 5.3k views
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Entering edit mode
11.9 years ago

I most certainly believe it is an internet connection problem that gives you this random behaviour. In your case, I would never try this over the network, as it is bound to fail at some point on such large files, due to classical network instability.

So yes, downloading this file is probably the solution.

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11.9 years ago
Michael 54k

Might be due to tabix, or not, but you seem to restrict to chromosome 1 via tabix, right? But the file already contains only chr1 data. You could therefore simply download the whole file with wget and see what happens.

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Yes, the restriction to chromosome 1 is redundant as the file only contains chromosome 1.

Downloading...

Thanks for the quick answers!

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9.9 years ago
siyu ▴ 150

I got the same error even when I download the remote VCF file. Did you find the answer??

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