Dpuiu snp: Difference between revisions
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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.soap -2 frag.single.soap -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.soap.sorted -d genome.fasta -o genome.cns | soapsnp -i frag.mated.soap.sorted -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 | |||
Revision as of 19:45, 25 May 2011
Soap
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 cat frag.mated.soap2 | sort -k8 -nk9 >! frag.mated.soap2.sorted mv frag.mated.soap2.sorted frag.mated.soap2 soapsnp -i frag.mated.soap.sorted -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