Dpuiu snp: Difference between revisions
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http://hapmap.ncbi.nlm.nih.gov | http://hapmap.ncbi.nlm.nih.gov | ||
Example: Landmark or Region:chr14:21100000..21199999 | 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 | |||
* 1000 genomes | * 1000 genomes | ||
Revision as of 17:06, 7 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
- 1000 genomes
http://www.1000genomes.org/
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