Re-sequencing
From Crop Genomics Lab.
bwa pipe
bowtie2 pipe
1. Make bowtie index
bowtie2-build reference.fa reference.fa |
2. Align
bowtie2-align -p num_threads -x reference_index -1 paired_1 -2 paired_2 -S sam_output |
3. convert sam to bam
samtools view -Sb <SAMFILE> > <BAMFILE> |
variation discovery
4. sort bam
5. bam index, fasta index
6. samtools mpileup -DSugf | bcftools -vcg -