From Crop Genomics Lab.
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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 -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg - <changed version, samtools mpileup -f scaffolds.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b bam_list | bcftools call -v -m -O v > variant.vcf>