Samtools

Setup output directory.

mkdir bowtie_samtools

If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.

cp bowtie/REL606.5.sam bowtie_samtools/ 
cp bowtie/REL606.5.fasta bowtie_samtools/

Index the reference file.

samtools faidx bowtie_samtools/REL606.5.fasta

Convert from SAM to BAM format.

samtools view -bS -o bowtie_samtools/REL606.5.bam bowtie/REL606.5.sam |borderStyle=solid}

Sort the BAM file.

samtools sort bowtie_samtools/REL606.5.bam bowtie_samtools/sorted_REL606.5

Output VCF file.

samtools mpileup -uf bowtie_samtools/REL606.5.fasta bowtie_samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> bowtie_samtools/output.vcf

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

h1. Determining Differences Between Aligners.Bedtools is a suite of utility programs that work on a variety of file formats, one of which is conveniently VCF format. Using *intersectBed* and *subtractBed* we can find equal and different predictions between mappers. Load Bedtools.{code

module load bedtools


Alike mutations.

intersectBed -a bowtie.vcf -b bwa.vcf > intersect.vcf


Unique mutations.

subtractBed -a bowtie.vcf -b intersect.vcf > unique_bowtie.vcf
subtractBed -a bwa.vcf -b intersect.vcf > unique_bowtie.vcf

Variant calling with Samtools

Samtools