Difference between revisions of "Re-sequencing"

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'''variation discovery'''
 
'''variation discovery'''
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4. sort bam
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5. bam index, fasta index
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6. mpileup -DSugf

Revision as of 02:16, 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. mpileup -DSugf