Dpuiu snp: Difference between revisions

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   U.S.: 30 trios ;residents with northern and western European ancestry
   U.S.: 30 trios ;residents with northern and western European ancestry


= 1000 genomes =
= 1,000 genomes =
* http://www.1000genomes.org/
* http://www.1000genomes.org/
* http://browser.1000genomes.org/index.html
* http://browser.1000genomes.org/index.html
= 10,000 genomes =
* http://genome10k.soe.ucsc.edu/


= Soap =
= Soap =

Revision as of 15:34, 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

 http://hapmap.ncbi.nlm.nih.gov
 Example: Landmark or Region:chr14:21100000..21199999
 270 people. 
 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

1,000 genomes

10,000 genomes

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