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Search: Posts Made By: laura
Forum: Bioinformatics 05-09-2016, 04:13 AM
Replies: 0
Views: 358
Posted By laura
The 1000 Genomes Project Data Portal Beta Release

We have produced a new tool to help users discover the data produced by the 1000 Genomes Project and managed by the International Genome Sample Resource (IGSR)
...
Forum: Bioinformatics 05-24-2014, 02:01 PM
Replies: 48
Views: 54,175
Posted By laura
vyellapa This is relevant to samtools and...

vyellapa

This is relevant to samtools and not to the VCF spec. I would recommend creating a new question about this or emailing the samtools help list you will get a better response this way
Forum: Bioinformatics 12-21-2013, 02:21 AM
Replies: 22
Views: 3,095
Posted By laura
You can do this with biomart Look at this...

You can do this with biomart

Look at this canned query
...
Forum: Bioinformatics 12-05-2013, 01:37 AM
Replies: 36
Views: 51,513
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, 12:28 AM
Replies: 36
Views: 51,513
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 06-23-2013, 10:18 AM
Replies: 21
Views: 2,580
Posted By laura
That would suggest the script isn't in the...

That would suggest the script isn't in the location where you are running the command from
Forum: Bioinformatics 06-19-2013, 12:31 AM
Replies: 21
Views: 2,580
Posted By laura
Can you give me specific coordinates that you are...

Can you give me specific coordinates that you are using and let me know where your 6777 count comes from

When I look at our vcf file in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/
...
Forum: Bioinformatics 06-18-2013, 12:52 AM
Replies: 21
Views: 2,580
Posted By laura
the vcf to ped form and script should not skip...

the vcf to ped form and script should not skip any variants which are variable in the individuals you ask it to consider

Can you give a specific example of the variants you think it is missing and...
Forum: Bioinformatics 06-04-2013, 10:50 PM
Replies: 21
Views: 2,580
Posted By laura
Apologies this is due to a typo in the example,...

Apologies this is due to a typo in the example, there is a space between the ftp directory and the filename where there should be a /
Forum: Bioinformatics 06-04-2013, 07:35 AM
Replies: 3
Views: 1,114
Posted By laura
The Ensembl VEP is a pretty cool tool You...

The Ensembl VEP is a pretty cool tool

You can also use it as a script and where available it also considered regulatory features
Forum: Bioinformatics 06-04-2013, 07:14 AM
Replies: 21
Views: 2,580
Posted By laura
Can you post your full command line and any error...

Can you post your full command line and any error messages you see so we can help
Forum: Bioinformatics 06-04-2013, 04:19 AM
Replies: 3
Views: 1,114
Posted By laura
I am afraid I don't know much about annovar but I...

I am afraid I don't know much about annovar but I will say the Ensembl Variant Effect Predictor should work find with Cow as there is an ensembl cow database

See
...
Forum: Bioinformatics 06-04-2013, 04:04 AM
Replies: 21
Views: 2,580
Posted By laura
Have you tried our example command lines from the...

Have you tried our example command lines from the faq

http://www.1000genomes.org/faq/how-do-i-get-sub-section-vcf-file
Forum: Bioinformatics 02-26-2013, 01:33 AM
Replies: 36
Views: 51,513
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 02-26-2013, 01:16 AM
Replies: 14
Views: 4,353
Posted By laura
The final call set for Phase 1 (1092 individuals)...

The final call set for Phase 1 (1092 individuals) you can find here:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/

Please have a look at the README:
...
Forum: Bioinformatics 02-15-2013, 02:13 AM
Replies: 17
Views: 7,326
Posted By laura
The best way to get a consensus sequence based on...

The best way to get a consensus sequence based on the 1000genomes project official snp set it to use the vcf file and the vcftools

Our genotypes can be found in our release directories, we always...
Forum: Bioinformatics 12-13-2012, 12:17 AM
Replies: 36
Views: 51,513
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, 11:49 AM
Replies: 36
Views: 51,513
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, 10:27 PM
Replies: 36
Views: 51,513
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, 10:17 AM
Replies: 36
Views: 51,513
Posted By laura
That is correct

That is correct
Forum: Bioinformatics 12-05-2012, 10:10 PM
Replies: 36
Views: 51,513
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, 01:29 PM
Replies: 36
Views: 51,513
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, 09:38 AM
Replies: 36
Views: 51,513
Posted By laura
do feel free to email [email protected] if you...

do feel free to email [email protected] 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, 07:19 AM
Replies: 36
Views: 51,513
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, 06:50 AM
Replies: 36
Views: 51,513
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...
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