Question: perl, vcf-subset: Broken VCF header, no column names?
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gravatar for severalorks
2.8 years ago by
severalorks90
severalorks90 wrote:

EDIT: I found I can also use Data Slicer from 1000Genomes browser tools to do what I need

I ran:

tabix -h /data/ALL.chrX.phase3_shapeit2_mvncall_integrated_v1b.20130502.genotypes.vcf.gz | perl vcf-subset -c HG00097 | bgzip -c > HG00097.vcf.gz

and got the error: Broken VCF header, no column names?. I was able to obtain a tabix file (an issue I already solved). Why is this error occurring? I've tried looking at this: https://sourceforge.net/p/vcftools/mailman/message/28163106/

But the suggestion, using head -20, doesn't work.

Ultimately, what I'm trying to do is this:

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr17.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz 17:1471000-1472000 | perl vcf-subset -c HG00098 | bgzip -c > HG00098.vcf.gz
tabix -p vcf HG00098.vcf.gz
cat ref.fa | vcf-consensus HG00098.vcf.gz > HG00098.fa

http://www.1000genomes.org/faq/are-there-any-fasta-files-containing-1000-genomes-variants-or-haplotypes/

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by severalorks90
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