VAT/dataSets

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Revision as of 16:07, 6 June 2011 (view source) Lukas.habegger (Talk | contribs) (→Data sets) ← Older edit		Revision as of 16:07, 6 June 2011 (view source) Lukas.habegger (Talk | contribs) (→Data sets) Newer edit →
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	== Data sets ==		== Data sets ==
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-	=== 1000 Genomes Project ===
	<center>[[#top|Top]]</center>		<center>[[#top|Top]]</center>
-	==== 1000 Genomes Pilot Project: Low coverage samples ====	+	=== 1000 Genomes Pilot Project: Low coverage samples ===
	- Data files		- Data files
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	<center>[[#top|Top]]</center>		<center>[[#top|Top]]</center>
-	==== 1000 Genomes Project, Phase I, chr22, SNP calls ====	+	=== 1000 Genomes Project, Phase I, chr22, SNP calls ===
	- Data files		- Data files

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Revision as of 16:07, 6 June 2011

VAT Main Page

Contents 1 Data sets 1.1 1000 Genomes Pilot Project: Low coverage samples 1.2 1000 Genomes Project, Phase I, chr22, SNP calls 2 Pre-processed GENCODE annotation sets

Data sets

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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

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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
- Detailed workflow

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Pre-processed GENCODE annotation sets

The pre-processed GENCODE annotation sets can be downloaded here.