VAT/dataSets
From GersteinInfo
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(→Main 1000 Genomes Project, Phase I, SNP calls) |
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==== 1000 Genomes Pilot Project: Low coverage samples ==== | ==== 1000 Genomes Pilot Project: Low coverage samples ==== | ||
| - | - Data files | + | - Data files |
- Source: pilot_data, release: 2010_07, FTP: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/ | - Source: pilot_data, release: 2010_07, FTP: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/ | ||
- Indels | - Indels | ||
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- [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/snps/CHBJPT.low_coverage.2010_07.genotypes.vcf.gz CHBJPT.low_coverage.2010_07.genotypes.vcf.gz] | - [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/snps/CHBJPT.low_coverage.2010_07.genotypes.vcf.gz CHBJPT.low_coverage.2010_07.genotypes.vcf.gz] | ||
- [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/snps/YRI.low_coverage.2010_07.genotypes.vcf.gz YRI.low_coverage.2010_07.genotypes.vcf.gz] | - [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/snps/YRI.low_coverage.2010_07.genotypes.vcf.gz YRI.low_coverage.2010_07.genotypes.vcf.gz] | ||
| - | - Annotation file | + | - Annotation file: [ftp://ftp.sanger.ac.uk/pub/gencode/release_3b/gencode.v3b.annotation.NCBI36.gtf.gz GENCODE (version 3b, hg18)] using CDS elements where ''gene_type = protein_coding'' and ''transcript_type = protein_coding'' |
| - | + | - Results: [http://dynamic.gersteinlab.org/people/lh372/dev/vat_cgi?mode=process&dataSet=1000genomes_lowCoverage VAT] | |
| - | - Results | + | |
| - | + | ||
<br> | <br> | ||
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==== 1000 Genomes Project, Phase I, SNP calls ==== | ==== 1000 Genomes Project, Phase I, SNP calls ==== | ||
| - | - Data files: release: 20100804, FTP: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ | + | - Data files |
| - | - SNPs | + | - Source: release: 20100804, FTP: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ |
| - | + | - 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 | + | - 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'' |
| - | + | - Results: [http://dynamic.gersteinlab.org/people/lh372/dev/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804 VAT] | |
| - | - Results | + | |
| - | + | ||
Revision as of 18:28, 8 March 2011
Contents |
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
1000 Genomes Project, Phase I, 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
