The pipeline for human whole exome sequencing with paired reads data
A, Align samples to genome (BWA): get BAM files
bowtie
1./bowtie -t -y -S hg18 -1 reads_1.fq -2 reads_2.fq reads.sam
SAM Tools
2.samtools view -bS reads.sam > reads.bam
3.samtools sort reads.bam reads.sorted.bam
4.samtools index reads.sorted.bam
B,SNP or indel analysis:
A, Align samples to genome (BWA): get BAM files
bowtie
1./bowtie -t -y -S hg18 -1 reads_1.fq -2 reads_2.fq reads.sam
SAM Tools
2.samtools view -bS reads.sam > reads.bam
3.samtools sort reads.bam reads.sorted.bam
4.samtools index reads.sorted.bam
B,SNP or indel analysis:
Comment