Dpuiu snp: Difference between revisions
Jump to navigation
Jump to search
(→Soap) |
No edit summary |
||
| Line 2: | Line 2: | ||
* [http://soap.genomics.org.cn/soapaligner.html soap2] & [http://soap.genomics.org.cn/soapsnp.html soapsnp] | * [http://soap.genomics.org.cn/soapaligner.html soap2] & [http://soap.genomics.org.cn/soapsnp.html soapsnp] | ||
* 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.soap2 -2 frag.single.soap2 -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 | ||
#/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 | soapsnp -i frag.mated.soap2 -d genome.fasta -o genome.cns | ||
= Samtools = | = 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 faidx genome.fasta | ||
samtools view -bt genome.fasta.fai frag.mated.sam >! frag.mated.bam | 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 | samtools mpileup -ugf genome.fasta frag.mated.bam | bcftools view -vcg - > genome.snps | ||
Revision as of 20:06, 25 May 2011
Soap
- 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