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 reference file.
samtools faidx samtools/REL606.5.fasta |
Convert SAM to BAM format.
samtools view -bS -o samtools/REL606.5.bam bowtie/REL606.5.sam |borderStyle=solid} |
Sort BAM file.
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 |
Produces output.vcf from Bowtie and output.vcf from BWA.
Move all 3 bam files and all 3 vcf files to lonestar
introduce bedtools.