VAT/dataSets: Difference between revisions
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==== | ==== 1000 Genomes Pilot Project: Low coverage samples ==== | ||
- Data files: | - Data files: | ||
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==== | ==== Main 1000 Genomes Project, Phase I, SNP calls ==== | ||
- Data files: | - Data files: release: 20100804, FTP: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ | ||
- SNPs | - SNPs | ||
- ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp | - [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz ALL.2of4intersection.20100804.genotypes.vcf.gz] | ||
- Annotation file | - Annotation file | ||
- [ftp://ftp.sanger.ac.uk/pub/gencode/ | - [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'' | ||
- Results | - Results | ||
- [http://dynamic.gersteinlab.org/people/lh372/dev/vat_cgi?mode=process&dataSet= | - [http://dynamic.gersteinlab.org/people/lh372/dev/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804 VAT] | ||
Revision as of 18:24, 8 March 2011
Data sets
1000 Genomes Project
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
Main 1000 Genomes Project, Phase I, SNP calls
- Data files: 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
