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Samtools

Setup output directory.

Code Block
mkdir samtools

...

Produces output.vcf from Bowtie and output.vcf from BWA.
Move all 3(question) bam files and all 3(question) vcf files to lonestar
introduce bedtools.

Developing a pipeline.

Entering all these commands to first create an alignment and then using Samtools to create a VCF format quickly becomes tedious... Let's create a simple bashscript to streamline things.

Mapping with Bowtie:

Code Block

#!/usr/bin/env bash

#Bowtie.
mkdir bowtie
bp_seqconvert --from genbank --to fasta <REL606.5.gbk > bowtie/REL606.5.fasta
bowtie-build bowtie/REL606.5.fasta bowtie/REL606.5
bowtie -t --sam bowtie/REL606.5 -1 SRR030257_1.fastq -2 SRR030257_2.fastq bowtie/REL606.5.sam

#Samtools
mkdir samtools
cp bowtie/REL606.5.sam samtools/ 
cp bowtie/REL606.5.fasta samtools/
samtools faidx samtools/REL606.5.fasta
samtools view -bS -o samtools/REL606.5.bam bowtie/REL606.5.sam
samtools sort samtools/REL606.5.bam samtools/sorted_REL606.5
samtools mpileup -uf samtools/REL606.5.fasta samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> samtools/output.vcf 

Mapping with BWA:

Code Block

#!/usr/bin/env bash

#BWA
mkdir -p bwa 
bp_seqconvert --from genbank --to fasta <REL606.5.gbk > bwa/REL606.5.fasta
bwa index bwa/REL606.5.fasta
bwa aln -f bwa/SRR030257_1.sai bwa/REL606.5.fasta SRR030257_1.fastq
bwa aln -f bwa/SRR030257_2.sai bwa/REL606.5.fasta SRR030257_2.fastq
bwa sampe -f bwa/REL606.5.sam bwa/REL606.5.fasta bwa/SRR030257_1.sai bwa/SRR030257_2.sai SRR030257_1.fastq SRR030257_2.fastq

#Samtools
mkdir samtools
cp bwa/REL606.5.sam samtools/ 
cp bwa/REL606.5.fasta samtools/
samtools faidx samtools/REL606.5.fasta
samtools view -bS -o samtools/REL606.5.bam bwa/REL606.5.sam 
samtools sort samtools/REL606.5.bam samtools/sorted_REL606.5
samtools mpileup -uf samtools/REL606.5.fasta samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> samtools/output.vcf