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Thread | Thread Starter | Forum | Replies | Last Post |
SPANNER (1000 genomes) | Margarida | Bioinformatics | 11 | 12-04-2013 09:09 AM |
1000 genomes - can anyone join in? | henry.wood | General | 0 | 06-24-2011 04:21 AM |
1000 Genomes Data | RichardRocca | General | 1 | 03-16-2011 12:11 PM |
1000 genomes | Nataiki | Bioinformatics | 4 | 02-04-2011 04:42 AM |
CoComputational Resources on Assembling Genomes | raghavagps | Bioinformatics | 0 | 01-17-2010 09:56 AM |
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#21 |
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Location: Boston, USA Join Date: Jan 2011
Posts: 20
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Laura,
how/what should I specify, if I don't have particular region to look at and want to get all genome-wide variants? Thanks so much for you kind help. |
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#22 |
Senior Member
Location: Cambridge UK Join Date: Sep 2008
Posts: 151
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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/ |
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#23 |
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Location: germany Join Date: Oct 2009
Posts: 140
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there is another paper with 113 pages, "supplemental information"
http://www.nature.com/nature/journal...re11632-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/Anal...mat-version-41 which is 19 pages Last edited by gsgs; 12-07-2012 at 07:15 AM. |
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#24 |
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Location: Boston, USA Join Date: Jan 2011
Posts: 20
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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: ![]() 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 |
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#25 |
Senior Member
Location: Cambridge UK Join Date: Sep 2008
Posts: 151
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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 |
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#26 |
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Location: Boston, USA Join Date: Jan 2011
Posts: 20
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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 |
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#27 |
Senior Member
Location: Cambridge UK Join Date: Sep 2008
Posts: 151
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Hello Rama
Unfortunately I can not recreate your issue Using your command I get a vcf file which just contains genotypes for NA10851 |
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#28 |
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Location: Boston, USA Join Date: Jan 2011
Posts: 20
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Thanks Laura, for trying it out.
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#29 |
Senior Member
Location: berd Join Date: Dec 2010
Posts: 179
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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, |
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#30 |
Member
Location: Oceania Join Date: May 2011
Posts: 11
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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, |
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#31 |
Senior Member
Location: Cambridge UK Join Date: Sep 2008
Posts: 151
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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 |
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#32 |
Senior Member
Location: Worcester, MA Join Date: Oct 2009
Posts: 133
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@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.
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#33 |
Junior Member
Location: Tunisia Join Date: Dec 2013
Posts: 4
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Please is there any one can help me how can I BLAST one FASTE file with more than 3000 sequences
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#34 |
Senior Member
Location: Cambridge UK Join Date: Sep 2008
Posts: 151
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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 |
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#35 |
Junior Member
Location: Tunisia Join Date: Dec 2013
Posts: 4
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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.
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#36 |
Senior Member
Location: Cambridge UK Join Date: Sep 2008
Posts: 151
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Start a new thread, this is not the right place for this question
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#37 |
Junior Member
Location: Brasil Join Date: Apr 2017
Posts: 2
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Hi Guys,
Fine? Has anyone read this article? Https://mediatum.ub.tum.de/doc/1094391/1094391.pdf I have question about ring buffer of this article... The page 11/12 the article explains for us that algorithm acess lines 14 and 15 of algorithm and posErr is with value k+1, but I was testing and the value is k and the algoritm Assumes negative values for the ring buffer posErr.... Can someone who knows this problem help me understand how to work with this ring buffer, or am I analyzing it wrong? Thanks |
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