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1000 Genomes Phase1 Integrated Release File

Hi,

I suspect recent 1000 genomes release 20110521 file is corrupted:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/

I am not able to unzip it either using gunzip, tabix or zcat. anyone ever try to unzip it before?

Can help to enlighten?

thanks

J

genome
• 2,359 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Jayce • Jayce

1 answer

It uses a modified gzip format called bgzip so it can be indexed with tabix: http://samtools.sourceforge.net/tabix.shtml

See also: How To Decompress 1000Genomes Bgzip-Compressed Files Using Java

• 1 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

exactly, i had tried many times and it doesnt work!!!:

~/installation/vcftools/bin/./tabix -f -h ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz > chr22.vcf

any idea?many thanks :)

• 0 views • link
updated by Ram Ram • written by Jayce • Jayce

and the error message:

[tabix] was bgzip used to compress this file? ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz

• 0 views • link
written by Jayce • Jayce

In my folder i have two files:

ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz    1.8 GB
ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz.tbi
• 0 views • link
updated by Ram Ram • written by Jayce • Jayce

What does file ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz says?

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Hi,

my command:

~/installation/vcftools/bin/./tabix -f -h ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz
• 0 views • link
updated by Ram Ram • written by Jayce • Jayce

it's the same as per what i downloaded

• 0 views • link
written by Jayce • Jayce

In two steps (?) first tabix -f file.vcf and then tabix -h [region]

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

In two steps (?) first tabix -p vcf -f file.vcf and then tabix -h [region]

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

In one step or two steps, it doesn't work either:

~/installation/vcftools/bin/./tabix -f ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz
[tabix] was bgzip used to compress this file? ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz
~/installation/vcftools/bin/./tabix -h ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz
[tabix] the index file exists. Please use '-f' to overwrite.

help...

• 0 views • link
updated by Ram Ram • written by Jayce • Jayce

I tried tabix -p vcf but doesn't work:

~/installation/vcftools/bin/./tabix -p vcf -f ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz 
[tabix] was bgzip used to compress this file? ALL.chr22.phase1_intergrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz
• 0 views • link
updated by Ram Ram • written by Jayce • Jayce

help help please????

• 0 views • link
written by Jayce • Jayce

i guess the file was corrupted during the download. i re-download it and it works...thanks :)

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written by Jayce • Jayce

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