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.
{expand:
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.
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 |