Difference between revisions of "Re-sequencing"
From Crop Genomics Lab.
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5. bam index, fasta index | 5. bam index, fasta index | ||
− | 6. samtools mpileup - | + | 6. samtools mpileup -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg - |
Revision as of 02:37, 11 December 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 -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg -