[Error] getting fasta file from 1000genomes

Question

[Mari]

Hi,

I'd like to get a fasta file of haplotypes from 1000 genomes.

I ran the commands below:

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

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.

[Matt Shirley]

Can you give some more information about how you tried to install vcf-tools?

[Mari]

Matt,

Thank you. I tried to run this:

marie@ubuntu:~/Downloads$ sudo apt-get install vcf-tools
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package vcf-tools

[Phil S.]

vcftools is not in the distrib software repo. You have to install it 'manually'. See here.

[Mari]

Thank you Phil, maybe I move ahead a bit but got another error.

marie@ubuntu:~/Downloads/vcftools_0.1.8a/perl$ 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] the index file is older than the vcf file. Please use '-f' to overwrite or reindex.
Broken VCF header, no column names?
 at /usr/share/perl5/Vcf.pm line 171
    Vcf::throw('Vcf4_1=HASH(0x160ee48)', 'Broken VCF header, no column names?') called at /usr/share/perl5/Vcf.pm line 845
    VcfReader::_read_column_names('Vcf4_1=HASH(0x160ee48)') called at /usr/share/perl5/Vcf.pm line 589
    VcfReader::parse_header('Vcf4_1=HASH(0x160ee48)') called at vcf-subset line 119
    main::vcf_subset('HASH(0x16051c8)') called at vcf-subset line 12

[Matt Shirley]

I think you can safely use the -f flag 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.

[Mari]

Thank you Matt, I added -f like this and the program ran:

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 -f

(Initially I tried to run the code below and it didn't work)

tabix -h -f 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

but at the last line, I got many errors:

cat ref.fa | vcf-consensus HG00098.vcf.gz > HG00098.fa

Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 3.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 3.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 3.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 3.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 3.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 3.
Note: Conflicting variants at (or near) ARRAY(0xb51bd0):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 4.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 4.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 4.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 4.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 4.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 4.
Note: Conflicting variants at (or near) ARRAY(0xcca2d8):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 5.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 5.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 5.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 5.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 5.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 5.
Note: Conflicting variants at (or near) ARRAY(0xcca260):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 6.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 6.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 6.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 6.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 6.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 6.
Note: Conflicting variants at (or near) ARRAY(0xcca2f0):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 7.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 7.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 7.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 7.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 7.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 7.
Note: Conflicting variants at (or near) ARRAY(0xcca290):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 8.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 8.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 8.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 8.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 8.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 8.
Note: Conflicting variants at (or near) ARRAY(0xcca2a8):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 9.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 9.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 9.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 9.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 9.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 9.
Note: Conflicting variants at (or near) ARRAY(0xcca380):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 10.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 10.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 10.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 10.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 10.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 10.
Note: Conflicting variants at (or near) ARRAY(0xcca458):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 11.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 11.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 11.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 11.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 11.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 11.
Note: Conflicting variants at (or near) ARRAY(0xcca4b8):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 12.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 12.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 12.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 12.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 12.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 12.
Note: Conflicting variants at (or near) ARRAY(0xcca440):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 13.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 13.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 13.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 13.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 13.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 13.
Note: Conflicting variants at (or near) ARRAY(0xcca4a0):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 14.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 14.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 14.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 14.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 14.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 14.
Note: Conflicting variants at (or near) ARRAY(0xcca428):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 15.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 15.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 15.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 15.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 15.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 15.
Note: Conflicting variants at (or near) ARRAY(0xcca488):, cannot apply both.
Use of uninitialized value in uc at /usr/share/perl5/Vcf.pm line 2831, <STDIN> line 16.
Use of uninitialized value $alt in pattern match (m//) at /usr/share/perl5/Vcf.pm line 2834, <STDIN> line 16.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 97, <STDIN> line 16.
Use of uninitialized value in addition (+) at vcf-consensus line 104, <STDIN> line 16.
Use of uninitialized value in numeric le (<=) at vcf-consensus line 179, <STDIN> line 16.
Use of uninitialized value in concatenation (.) or string at vcf-consensus line 181, <STDIN> line 16.
Note: Conflicting variants at (or near) ARRAY(0xcca410):, cannot apply both.

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