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Forum: Bioinformatics 12-05-2013, 02:37 AM
Replies: 37
Views: 88,734
Posted By laura
Start a new thread, this is not the right place...

Start a new thread, this is not the right place for this question
Forum: Bioinformatics 12-05-2013, 01:28 AM
Replies: 37
Views: 88,734
Posted By laura
Mokhtar you would be better creating a new thread...

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...
Forum: Bioinformatics 02-26-2013, 02:33 AM
Replies: 37
Views: 88,734
Posted By laura
These two data sets represent our most recent set...

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...
Forum: Bioinformatics 12-13-2012, 01:17 AM
Replies: 37
Views: 88,734
Posted By laura
Hello Rama Unfortunately I can not recreate...

Hello Rama

Unfortunately I can not recreate your issue

Using your command I get a vcf file which just contains genotypes for NA10851
Forum: Bioinformatics 12-07-2012, 12:49 PM
Replies: 37
Views: 88,734
Posted By laura
You need to give tabix some sort of chromosome...

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...
Forum: Bioinformatics 12-06-2012, 11:27 PM
Replies: 37
Views: 88,734
Posted By laura
You can give tabix a whole chromosome but be...

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...
Forum: Bioinformatics 12-06-2012, 11:17 AM
Replies: 37
Views: 88,734
Posted By laura
That is correct

That is correct
Forum: Bioinformatics 12-05-2012, 11:10 PM
Replies: 37
Views: 88,734
Posted By laura
You should be able to get this info from our vcf...

You should be able to get this info from our vcf files using a combination of tabix anc vcftools vcf-subset as described in our faq

http://www.1000genomes.org/faq/how-do-i-get-slice-your-vcf-files
Forum: Bioinformatics 12-05-2012, 02:29 PM
Replies: 37
Views: 88,734
Posted By laura
As far as chrY ...

As far as chrY

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ALL.chrY.phase1_samtools_si.20101123.snps.low_coverage.genotypes.vcf.gz
...
Forum: Bioinformatics 12-05-2012, 10:38 AM
Replies: 37
Views: 88,734
Posted By laura
do feel free to email info@1000genomes.org if you...

do feel free to email info@1000genomes.org if you have any questions

We do also have a recent set of slides which were presented in a tutorial at ASHG2012
...
Forum: Bioinformatics 12-05-2012, 08:19 AM
Replies: 37
Views: 88,734
Posted By laura
I would strongly recommend starting with our...

I would strongly recommend starting with our recent paper and the analysis results associated with it

http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html
...
Forum: Bioinformatics 12-05-2012, 07:50 AM
Replies: 37
Views: 88,734
Posted By laura
What would you like to do with the data, that...

What would you like to do with the data, that will very much determine what the best way to approach the data set,

1000 genomes is a large data set with a variety of different data formats but to...
Forum: Bioinformatics 07-02-2012, 02:51 AM
Replies: 37
Views: 88,734
Posted By laura
http://www.1000genomes.org/announcements/phase-1-a...

http://www.1000genomes.org/announcements/phase-1-analysis-results-including-chry-and-chrmt-variant-calls-2012-07-02

A relatively complete set of variant and other files associated with our Phase 1...
Forum: Bioinformatics 03-01-2012, 03:17 AM
Replies: 37
Views: 88,734
Posted By laura
We now have a tutorial about using 1000 genomes...

We now have a tutorial about using 1000 genomes data

http://www.1000genomes.org/announcements/using-1000-genomes-data-tutorial-2012-03-01
Forum: Bioinformatics 09-01-2011, 07:30 AM
Replies: 37
Views: 88,734
Posted By laura
Our browser has been updated to version 63 of the...

Our browser has been updated to version 63 of the ensembl code and we have a new Variation Pattern Finder tool to go along slide it
...
Forum: Bioinformatics 06-16-2011, 06:38 AM
Replies: 37
Views: 88,734
Posted By laura
We have also now added a public mysql instance...

We have also now added a public mysql instance for the ensembl databases which back our browser

You can find more details of this on http://www.1000genomes.org/public-ensembl-mysql-instance
Forum: Bioinformatics 05-09-2011, 05:42 AM
Replies: 37
Views: 88,734
Posted By laura
New Resources for 1000 Genomes

New Resources for 1000 Genomes

General Info

As well as posting new announcements on the front page of http://www.1000genomes.org, we have both rss...
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