From Crop Genomics Lab.
Revision as of 02:16, 11 February 2015 by Alima90 (Talk | contribs)

Jump to: navigation, search

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. mpileup -DSugf