Dpuiu snp: Difference between revisions
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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 | soapsnp -i frag.mated.soap -d genome.fasta -o genome.cns | ||
= Samtools = | = Samtools = | ||
Revision as of 19:46, 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 -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