New Resources for 1000 Genomes

[laura]

Start a new thread, this is not the right place for this question

[Mokhtar]

Please is there any one can help me how can I BLAST one FASTE file with more than 3000 DNA sequences generated from fungus community.

[laura]

Mokhtar you would be better creating a new thread for your question, this isnt really related to the 1000 genomes project

If you let people know what your sequences (dna, cdna, protein?) are and what species you are working in they will probably be able to offer better advice

[Mokhtar]

Please is there any one can help me how can I BLAST one FASTE file with more than 3000 sequences

[jgibbons1]

@papori I had the same issue. You can download the "sequence.index" file from the ftp site (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/). In Excel, I ended up making a new column where I divided BASE_COUNT by READ_COUNT. You can then filter the read length you are looking for.

[laura]

These two data sets represent our most recent set of alignments and the frozen alignments used for the phase1 analysis effort

There will be overlapping individuals between the two sets but no bam files should be the same as an extended version of GRCh37 is being used for the post phase1 mapping

see http://www.1000genomes.org/faq/which...bly-do-you-use

You should be able to tell the difference between these files by the YYYYMMDD in their name as this points to the sequence index they were based on

[southan]

I'm going to download Bam files from the Project.
I see two links:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/
and
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/

There are some overlapping files between the two links.

I would like to know which one I should use?

Thanks,

[papori]

Hi,
Sorry if this is already been asked, I didn't find it..

I try to figure out if I can do a search by read length.
I am looking for reads length 101.
Is there a way to know this information before downloading?
I looked in the sequence.index but I didn't find this.

Thanks in advance,
Pap

Thanks,

[rama]

Thanks Laura, for trying it out.

[laura]

Hello Rama

Unfortunately I can not recreate your issue

Using your command I get a vcf file which just contains genotypes for NA10851

[rama]

Hi Laura,

I am still having trouble with extracting the variant calls of a specific sample.

As you pointed out earlier that I have downloaded sites file with no genotype column, so now I got this version ALL.2of4intersection.20100804.genotypes.vcf.gz vcf and tbi file from ftp site (release/20100804).

and I used the following command to subset the vcf file

tabix -fh /Volumes/Macintosh_HD_3/1000Genome/ALL.2of4intersection.20100804.genotypes.vcf.gz 1 | perl ~/othertools/vcftools_0.1.10/perl/vcf-subset -c NA10851 > NA10851/NA10851_chr1

but strangely the out-put file has all genotype columns. I have been following the directions given on the 1000 genome except the I don't give the range for chromosome as I want to get all variants. So I tried with giving the coordinates (see below) and result file has just the header only.

here is the command i used,
tabix -fh /Volumes/Macintosh_HD_3/1000Genome/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:1-243199373 | perl ~/othertools/vcftools_0.1.10/perl/vcf-subset -c NA10851 > NA10851/NA10851_chr2

so now I really don't know what I am doing wrong in trying to subset the vcf file. I really appreciate for your kind help so far and would be very grateful if you could help me how to solve this.

thank you so much.
Rama

[laura]

You need to give tabix some sort of chromosome name otherwise it doesn't know what to fetch

If you just want to filter the whole file you will need to use zcat

That being said you downloaded the sites file which contains no genotype info and no columns with individual genotypes to filter

[rama]

Laura,

I tried with downloading both the vcf.gz and tbi files. but it did not work and it is difficult to interpret the error. can you see what I am doing wrong here

./tabix -h /Volumes/Macintosh\ HD\ 3/1000Genome/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz | perl ~/othertools/vcftools_0.1.10/perl/vcf-subset -c NA10851

[tabix] the index file exists. Please use '-f' to overwrite.
Broken VCF header, no column names?
at /Users/molpathuser1/othertools/vcftools_0.1.10/perl//Vcf.pm line 177
Vcf::throw('Vcf4_1=HASH(0x7fa9d982f8d8)', 'Broken VCF header, no column names?') called at /Users/molpathuser1/othertools/vcftools_0.1.10/perl//Vcf.pm line 869
VcfReader::_read_column_names('Vcf4_1=HASH(0x7fa9d982f8d8)') called at /Users/molpathuser1/othertools/vcftools_0.1.10/perl//Vcf.pm line 604
VcfReader:arse_header('Vcf4_1=HASH(0x7fa9d982f8d8)') called at /Users/molpathuser1/othertools/vcftools_0.1.10/perl/vcf-subset line 122
main::vcf_subset('HASH(0x7fa9d98288f0)') called at /Users/molpathuser1/othertools/vcftools_0.1.10/perl/vcf-subset line 12

many thanks for your kind help

[gsgs]

there is another paper with 113 pages, "supplemental information"

http://www.nature.com/nature/journal/v491/n7422/extref/nature11632-s1.pdf

with a referrence:

...
38!
Garrison,!E.!K.!vcflib$K$a$simple$C++$library$for$parsing$and$manipulating$
VCF$files,!<https://github.com/ekg/vcflib>!(2012).!

pointing back to :

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

which is 19 pages

[laura]

You can give tabix a whole chromosome but be aware tabix can not cope with losed network connectivity so when streaming large data volumes that can cause lossed data which means you may need to download the whole file

http://www.biostars.org/p/50752/