Difference between revisions of "Re-sequencing"
From Crop Genomics Lab.
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4. sort bam | 4. sort bam | ||
+ | |||
5. bam index, fasta index | 5. bam index, fasta index | ||
− | 6. mpileup -DSugf | + | |
+ | 6. samtools mpileup -DSugf | bcftools -vcg - |
Revision as of 02:18, 11 February 2015
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 -