Dpuiu snp

Links

• IUPAC ambiguity codes
• NCBI SNP FTP

• Human Genome Assembly Information
• UC Santa Cruz Genome Browser
• 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

 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

• http://www.1000genomes.org/
• http://browser.1000genomes.org/index.html

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.

• I5K Insects

Soap

• soap2 & soapsnp

• 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