VAT/dataSets
From GersteinInfo
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- [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: [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'' | - 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 | + | - Results: [http://dynamic.gersteinlab.org/people/lh372/vat_cgi?mode=process&dataSet=1000genomes_lowCoverage&annotationSet=gencode3b&type=coding VAT] |
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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'' | ||
| - | - Results: [http://dynamic.gersteinlab.org/people/lh372 | + | - Results: [http://dynamic.gersteinlab.org/people/lh372/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804.chr22&annotationSet=gencode3c&type=coding VAT] |
- [http://info.gersteinlab.org/VAT#Example_workflow Detailed workflow] | - [http://info.gersteinlab.org/VAT#Example_workflow Detailed workflow] | ||
Latest revision as of 18:25, 14 June 2011
Contents |
Data sets
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, 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
Pre-processed GENCODE annotation sets
The pre-processed GENCODE annotation sets can be downloaded here.
