Dpuiu snp: Difference between revisions

From Cbcb
Jump to navigation Jump to search
Line 3: Line 3:
* [http://droog.gs.washington.edu/parc/images/iupac.html IUPAC ambiguity codes]
* [http://droog.gs.washington.edu/parc/images/iupac.html IUPAC ambiguity codes]
* [ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ NCBI SNP FTP]
* [ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ NCBI SNP FTP]
* [http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/?build=37 Human Genome Assembly Information]
* [http://genome.ucsc.edu/cgi-bin/hgTracks UC Santa Cruz Genome Browser]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp Entrez dbSNP]


= Soap =
= Soap =

Revision as of 19:33, 1 June 2011

Links

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