Dpuiu snp

Soap

• soap2 & soapsnp
• Example:

 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