#Tools required (Slide 4) #samtools http://samtools.sourceforge.net/ #Tabix (Slide 4) http://sourceforge.net/projects/samtools/files/tabix/ svn co https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/tabix #VCFtools (Slide 4) http://vcftools.sourceforge.net/ #The ensembl variation and core apis (Slide 4) http://www.ensembl.org/index.html #The variant effect predictor (Slide 4) ftp://ftp.ensembl.org/pub/misc-scripts/Variant_effect_predictor/ #The variation pattern finder (Slide 4) ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/browser/variation_pattern_finder/version_1.0 #VCF to PED Converter (Slide 4) ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/browser/vcf_to_ped_converter/version_1.0/ #Haploview (Slide 4) http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/downloads #EBI FTP url (slide 22) ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/ #1000 genomes website (slide 22) http://www.1000genomes.org #1000 genomes ensembl style browser (slide 22) http://browser.1000genomes.org #samtools view command line with HG01375 (Slide 34) #Please note the http url. This is because samtools streams better across http than it does over #ftp samtools view http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG01375/alignment/HG01375.mapped.ILLUMIA.bwa.CLM.low_coverage.20111114.bam 6:31833200-31834200 #tabix command line to get section of Omni genotypes (Slide 34) tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120131_omni_genotypes_and_intensities/Omni25_genotypes_2141_samples.b37.vcf.gz 6:31833200-31834200 #Getting the current tree file (Slide 38) wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree #Grep for the omni vcf file (Slide 38) grep omni current.tree | grep vcf | grep 2012 | grep -v tbi | cut -f1 #Tabix to get the specifed region (Slide 38) tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120131_omni_genotypes_and_intensities/Omni25_genotypes_2141_samples.b37.vcf.gz 6:31831625-31834704 #grep to get the HG01375 bam (Slide 38) grep HG01375 current.tree | grep low_coverage | grep mapped | grep -v bai | grep -v bas | grep -v unmapped | cut -f1 #samtools to view the section of the bam file (Slide 38) samtools view http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG01375/alignment/HG01375.mapped.ILLUMINA.bwa.CLM.low_coverage.20111114.bam 6:31831625-31834704 #Example VCF file to be uploaded to the browser (Slide 47) ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.wgs.phase1_release_v2.20101123.snps_indels_sv.sites.vcf.gz #Example BAM file to be uploaded to browser (Slide 48) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG01375/alignment/HG01375.mapped.ILLUMINA.bwa.CLM.low_coverage.20111114.bam #Browser url (Slide 57) http://browser.1000genomes.org #URL for Variant Effect Predictor Script (Slide 62) ftp://ftp.ensembl.org/pub/misc-scripts/Variant_effect_predictor/ #Variant Effect Predictor Command line (Slide 63) perl variant_effect_predictor.pl -input 6_381831625_3184704.vcf -sift p -polyphen p –check_existing #Viewing output file from the Variant Effect Predictor (Slide 63) less variant_effect_output.txt #Getting a slice of bam file (Slide 64) samtools view http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG01375/alignment/HG01375.mapped.ILLUMINA.bwa.CLM.low_coverage.20111114.bam 6:31833625-31833704 #Getting a slice of a vcf file (Slide 64) tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120131_omni_genotypes_and_intensities/Omni25_genotypes_2141_samples.b37.vcf.gz 6:31830969-31846823 | vcf-subset -c HG01375 #URL for Data Slicer on website (Slide 64) http://browser.1000genomes.org/Homo_sapiens/UserData/SelectSlice #URL for Variation Pattern Finder (Slide 65) http://browser.1000genomes.org/Homo_sapiens/UserData/VariationsMapVCF #Command line for Variation Pattern Finder (Slide 66) perl variant_pattern_finder.pl -vcf ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr6.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz -sample_panel_file ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel -region 6:31830969-31846823 -expand #URL for VCF to PED conversion tool (Slide 68) http://browser.1000genomes.org/Homo_sapiens/UserData/Haploview #Command line for VCF to PED conversion (Slide 69) perl vcf_to_ped_convert.pl -vcf ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr6.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz -sample_panel_file ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel -region 6:31830969-31846823 -population CEU #URL for Haploview (Slide 70) http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview #URL for Variation API Ensembl 63 (Slide 71) http://jun2011.archive.ensembl.org/info/docs/api/variation/index.html #URL for Variation API Current (Slide 71) http://www.ensembl.org/info/docs/api/variation/index.html #URL for 1000 Genomes Public Mysql Instance details (Slide 71) http://www.1000genomes.org/node/517 #URL for Release chr6 file (Slide 73) ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr6.phase1_release_v2.20101123.snps_indels_svs.vcf.gz #Tabix command to get slice of release file (Slide 74) tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr6.phase1_release_v2.20101123.snps_indels_svs.vcf.gz 6:31831625-31834704 > 6_381831625_3184704.vcf #Variant Effect Predictor command to get sift and polyphen values for the snps (Slide 74) perl variant_effect_predictor.pl -input 6_381831625_3184704.vcf -sift p -polyphen p -check_existing #Variant Pattern Finder tool command to get patterns for same region (Slide 74) perl variant_pattern_finder.pl -vcf ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr6.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz -sample_panel_file ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel -region 6:31831625-31834704 -expand #VCF to PED command to get ped and info file for this region (Slide 74) perl vcf_to_ped_convert.pl -vcf ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr6.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz -sample_panel_file ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel -region 6:31830969-31846823 -population CEU #1000 Genomes Website (Slide 76) http://1000genomes.org #1000 Genomes Annoucements mailing list (Slide 76) 1000announce@1000genomes.org #URL for Announce email subscription (Slide 76) http://www.1000genomes.org/1000-genomes-annoucement-mailing-list #URL for RSS feed for annoucements (Slide 76) http://www.1000genomes.org/announcements/rss.xml #URL for 1000genomes twitter feed (Slide 76) http://twitter.com/#!/1000genomes #Help email address (Slide 76) info@1000genomes.org