Dpuiu snp: Difference between revisions

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* Example:
* Example:
   2bwt-builder genome.fasta
   2bwt-builder genome.fasta
   soap2 –a frag_1.fastq -b frag_2.fastq -D genome.fasta.index -o frag.mated.soap -2 frag.single.soap -m 120 -x 240
   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
   cat frag.mated.soap2 | sort -k8 -nk9 >! frag.mated.soap2.sorted
   mv frag.mated.soap2.sorted frag.mated.soap2  
   mv frag.mated.soap2.sorted frag.mated.soap2  
   soapsnp -i frag.mated.soap -d genome.fasta -o genome.cns
   soapsnp -i frag.mated.soap2 -d genome.fasta -o genome.cns


= Samtools =
= Samtools =

Revision as of 19:47, 25 May 2011

Soap

 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

Samtools

 soap2sam.pl < frag.mated.soap2 > frag.mated.sam
 samtools faidx genome.fasta
 samtools view -bt genome.fasta.fai frag.mated.sam >! frag.mated.bam
 samtools mpileup -ugf genome.fasta frag.mated.bam | bcftools view -vcg - > genome.snps