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/
Prepare reference file.
samtools faidx samtools/REL606.5.fasta
Prepare alignment file.
Convert SAM to BAM format.
samtools view -bS -o samtools/REL606.5.bam bowtie/REL606.5.sam
[samopen] SAM header is present: 1 sequences.
Sort BAM file.
samtools sort samtools/REL606.5.bam samtools/sorted_REL606.5
[bam_sort_core] merging from 2 files...
Variant call output.
samtools mpileup -uf samtools/REL606.5.fasta samtools/sorted_REL606.5.bam
[mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 [bcfview] 100000 sites processed. [afs] 0:99910.349 1:52.764 2:36.886 [bcfview] 200000 sites processed. [afs] 0:99946.543 1:48.457 2:5.000 [bcfview] 300000 sites processed. [afs] 0:99976.591 1:5.410 2:17.999 [bcfview] 400000 sites processed. [afs] 0:99984.243 1:8.357 2:7.399 [bcfview] 500000 sites processed. [afs] 0:99970.803 1:23.197 2:6.000 [afs] 0:63952.773 1:6.227 2:2.000
Produces output.vcf from Bowtie and output.vcf from BWA.
Move all 3
bam files and all 3 vcf files to lonestar
introduce bedtools.