Dpuiu snp: Difference between revisions
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= Links = | |||
* [http://droog.gs.washington.edu/parc/images/iupac.html IUPAC ambiguity codes] | |||
* [ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ NCBI SNP FTP] | |||
* [http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/?build=37 Human Genome Assembly Information] | |||
* [http://genome.ucsc.edu/cgi-bin/hgTracks UC Santa Cruz Genome Browser] | |||
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp Entrez dbSNP] | |||
Search examples: | |||
14[CHR] AND "human"[ORGN] => 908,625 SNPS | |||
* Human dataset | |||
http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?sample=SRS000090# | |||
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878 | |||
= International Hapmap = | |||
* 270 people, 4 populations | |||
Yoruba people of Ibadan, Nigeria: 30 trios | |||
Japan, 45 unrelated individuals from the Tokyo area | |||
China, 45 unrelated individuals from Beijing | |||
U.S.: 30 trios ;residents with northern and western European ancestry | |||
* http://hapmap.ncbi.nlm.nih.gov | |||
* Example: | |||
Landmark or Region:chr14:21100000..21199999 | |||
= 1,000 genomes = | |||
* 2500 people, 25 populations | |||
* http://www.1000genomes.org/ | |||
* http://browser.1000genomes.org/index.html | |||
* [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40 Variant Call Format] | |||
= Personal Genome Project = | |||
* 100,000 humans | |||
* http://www.personalgenomes.org/ | |||
= 10,000 genomes = | |||
* [http://genome10k.soe.ucsc.edu/ G10K] | |||
* [http://jhered.oxfordjournals.org/content/100/6/659.full.pdf G10K paper] | |||
* Assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. | |||
* 16,203 representative vertebrate species out of ca. 60,000 living species | |||
* [http://www.arthropodgenomes.org/wiki/i5K I5K] Insects | |||
* [http://www.medpedia.com/news_analysis/6-Genomics-Evolution-and-Pseudoscience/entries/8989-10000-genomes-ndash-why Blog] | |||
= Soap = | = Soap = | ||
* [http://soap.genomics.org.cn/soapaligner.html soap2] & [http://soap.genomics.org.cn/soapsnp.html soapsnp] | * [http://soap.genomics.org.cn/soapaligner.html soap2] & [http://soap.genomics.org.cn/soapsnp.html soapsnp] | ||
* Example: | * Example: | ||
2bwt-builder genome.fasta | 2bwt-builder genome.fasta | ||
soap2 –a frag_1.fastq -b frag_2.fastq -D genome.fasta.index -o frag.mated. | |||
soap2 –a frag_1.fastq -b frag_2.fastq -D genome.fasta.index -o frag.mated.soap2 -2 frag.single.soap2 -m 120 -x 240 | |||
cat frag.mated.soap2 | sort -k8 -nk9 >! frag.mated.soap2.sorted | cat frag.mated.soap2 | sort -k8 -nk9 >! frag.mated.soap2.sorted | ||
mv frag.mated.soap2.sorted frag.mated.soap2 | mv frag.mated.soap2.sorted frag.mated.soap2 | ||
soapsnp -i frag.mated. | |||
soapsnp -i frag.mated.soap2 -d genome.fasta -o genome.cns | |||
= Samtools = | = Bowtie/Samtools = | ||
bowtie-build genome.fasta genome.fasta | |||
samtools | bowtie genome.fasta -1 frag_1.fastq -2 frag_2.fastq -p 8 -I 120 -X 240 --sam > frag.mated.sam | ||
samtools | |||
samtools view -bS frag.mated.sam > frag.mated.bam | |||
samtools sort frag.mated.bam frag.mated.bam.sorted | |||
mv frag.mated.bam.sorted frag.mated.bam | |||
samtools mpileup -ugf genome.fasta frag.mated.bam | bcftools view -vcg - > genome.snps | samtools mpileup -ugf genome.fasta frag.mated.bam | bcftools view -vcg - > genome.snps | ||
Latest revision as of 16:33, 14 June 2011
Links
Search examples: 14[CHR] AND "human"[ORGN] => 908,625 SNPS
- Human dataset
http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?sample=SRS000090# http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878
International Hapmap
- 270 people, 4 populations
Yoruba people of Ibadan, Nigeria: 30 trios Japan, 45 unrelated individuals from the Tokyo area China, 45 unrelated individuals from Beijing U.S.: 30 trios ;residents with northern and western European ancestry
- http://hapmap.ncbi.nlm.nih.gov
- Example:
Landmark or Region:chr14:21100000..21199999
1,000 genomes
- 2500 people, 25 populations
- http://www.1000genomes.org/
- http://browser.1000genomes.org/index.html
- Variant Call Format
Personal Genome Project
- 100,000 humans
- http://www.personalgenomes.org/
10,000 genomes
- G10K
- G10K paper
- Assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus.
- 16,203 representative vertebrate species out of ca. 60,000 living species
- I5K Insects
- Blog
Soap
- Example:
2bwt-builder genome.fasta soap2 –a frag_1.fastq -b frag_2.fastq -D genome.fasta.index -o frag.mated.soap2 -2 frag.single.soap2 -m 120 -x 240 cat frag.mated.soap2 | sort -k8 -nk9 >! frag.mated.soap2.sorted mv frag.mated.soap2.sorted frag.mated.soap2 soapsnp -i frag.mated.soap2 -d genome.fasta -o genome.cns
Bowtie/Samtools
bowtie-build genome.fasta genome.fasta bowtie genome.fasta -1 frag_1.fastq -2 frag_2.fastq -p 8 -I 120 -X 240 --sam > frag.mated.sam samtools view -bS frag.mated.sam > frag.mated.bam samtools sort frag.mated.bam frag.mated.bam.sorted mv frag.mated.bam.sorted frag.mated.bam samtools mpileup -ugf genome.fasta frag.mated.bam | bcftools view -vcg - > genome.snps