Difference between revisions of "Re-sequencing"

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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 -