Difference between revisions of "Re-sequencing"

Revision as of 01:51, 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 -DSugf | bcftools view -vcg -

Revision as of 02:18, 11 February 2015 (view source) Alima90 (Talk \| contribs) ← Older edit		Revision as of 01:51, 11 December 2015 (view source) Alima90 (Talk \| contribs) Newer edit →
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	5. bam index, fasta index		5. bam index, fasta index

−	6. samtools mpileup -DSugf \| bcftools -vcg -	+	6. samtools mpileup -DSugf \| bcftools view -vcg -