Entering edit mode
8.7 years ago
Mari ▴ 30
I'd like to get a fasta file of haplotypes from 1000 genomes.
I ran the commands below:
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
but got error massages,
[tabix] the index file is older than the vcf file. Please use '-f' to overwrite or reindex. Can't open perl script "vcf-subset": No such file or directory
And when I tried to install vcf-tools, I got
E: Unable to locate package vcf-tools
How can I run these commands successfully?
My machine is Ubuntu 64 bit on Win7.0.
Can you give some more information about how you tried to install vcf-tools?
Thank you. I tried to run this:
vcftools is not in the distrib software repo. You have to install it 'manually'. See here.
Thank you Phil, maybe I move ahead a bit but got another error.
I think you can safely use the
-fflag that tabix is warning you about. Currently it looks like tabix is not returning any data - you can check this by simply omitting everything after and including your first pipe character.
Thank you Matt, I added
-flike this and the program ran:
(Initially I tried to run the code below and it didn't work)
but at the last line, I got many errors: