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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(question) bam files and all 3(question) vcf files to lonestar
introduce bedtools.

Developing a pipeline.

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