Dpuiu snp: Difference between revisions
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http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?sample=SRS000090# | http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?sample=SRS000090# | ||
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878 | 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 | |||
= Soap = | = Soap = | ||
Revision as of 20:00, 2 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
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