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