Samtools
Setup output directory.
mkdir 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 samtools/ cp bowtie/REL606.5.fasta samtools/
Index the reference file.
samtools faidx samtools/REL606.5.fasta
Convert from SAM to BAM format.
samtools view -bS -o samtools/REL606.5.bam bowtie/REL606.5.sam |borderStyle=solid}
Sort the BAM file.
samtools sort samtools/REL606.5.bam samtools/sorted_REL606.5
Output VCF file.
samtools mpileup -uf samtools/REL606.5.fasta samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> 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.