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.
module load bedtools
Finding alike mutations.
intersectBed -a bowtie.vcf -b bwa.vcf > intersect.vcf
Finding unique mutations for each mapper.
subtractBed -a bowtie.vcf -b intersect.vcf > unique_bowtie.vcf
subtractBed -a bwa.vcf -b intersect.vcf > unique_bowtie.vcf