Dpuiu snp

Links

• IUPAC ambiguity codes
• NCBI SNP FTP

Soap

• soap2 & soapsnp

• 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 
 #/fs/szdevel/core-cbcb-software/Linux-x86_64/bin/soap2sam.pl < frag.mated.soap2 > frag.mated.sam
 
 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 faidx genome.fasta
 samtools view -bt genome.fasta.fai frag.mated.sam >! frag.mated.bam

 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