VAT/dataSets

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(1000 Genomes Project, Phase I, SNP calls)
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<center>[[#top|Top]]</center>
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==== 1000 Genomes Project, Phase I, SNP calls ====
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==== 1000 Genomes Project, Phase I, chr22, SNP calls ====
  - Data files
  - Data files
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     - SNPs: [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz ALL.2of4intersection.20100804.genotypes.vcf.gz]
     - SNPs: [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz ALL.2of4intersection.20100804.genotypes.vcf.gz]
  - Annotation file: [ftp://ftp.sanger.ac.uk/pub/gencode/release_3c/gencode.v3c.annotation.GRCh37.gtf.gz GENCODE (version 3c, hg19)] using CDS elements where ''gene_type = protein_coding'' and ''transcript_type = protein_coding''
  - Annotation file: [ftp://ftp.sanger.ac.uk/pub/gencode/release_3c/gencode.v3c.annotation.GRCh37.gtf.gz GENCODE (version 3c, hg19)] using CDS elements where ''gene_type = protein_coding'' and ''transcript_type = protein_coding''
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  - Results: [http://dynamic.gersteinlab.org/people/lh372/dev/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804 VAT]
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  - Results: [http://dynamic.gersteinlab.org/people/lh372/dev/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804.chr22 VAT]

Revision as of 17:28, 9 March 2011

VAT Main Page

Contents


Data sets

1000 Genomes Project

Top

1000 Genomes Pilot Project: Low coverage samples

- Data files
    - Source: pilot_data, release: 2010_07, FTP:  ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/
    - Indels
        - CEU.low_coverage.2010_07.indel.genotypes.vcf.gz
        - JPTCHB.low_coverage.2010_07.indel.genotypes.vcf.gz
        - YRI.low_coverage.2010_07.indel.genotypes.vcf.gz
    - SNPs
        - CEU.low_coverage.2010_07.genotypes.vcf.gz
        - CHBJPT.low_coverage.2010_07.genotypes.vcf.gz
        - YRI.low_coverage.2010_07.genotypes.vcf.gz
- Annotation file: GENCODE (version 3b, hg18) using CDS elements where gene_type = protein_coding and transcript_type = protein_coding
- Results: VAT


Top

1000 Genomes Project, Phase I, chr22, SNP calls

- Data files
    - Source: release: 20100804, FTP: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/
    - SNPs: ALL.2of4intersection.20100804.genotypes.vcf.gz
- Annotation file: GENCODE (version 3c, hg19) using CDS elements where gene_type = protein_coding and transcript_type = protein_coding
- Results: VAT
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