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Code Block
cp bowtie/REL606.5.sam samtools/ 
cp bowtie/REL606.5.fasta samtools/

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Index reference file.

Code Block
title

samtools faidx samtools/REL606.5.fasta
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Prepare alignment file.


Convert SAM to BAM format.

Code Block
title

samtools view -bS -o samtools/REL606.5.bam bowtie/REL606.5.sam
 |borderStyle
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[samopen] SAM header is present: 1 sequences.
=solid}

Sort BAM file.

Code Block
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samtools sort samtools/REL606.5.bam samtools/sorted_REL606.5
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[bam_sort_core] merging from 2 files...

Variant call output.

samtools mpileup -uf
Code Block
1bcftools view -vcg - > samtools/output.vcf
title

samtools mpileup -uf samtools/REL606.5.fasta samtools/sorted_REL606.5.bam
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[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 \|bcftools view -vcg - \> samtools/output.vcf 

Produces output.vcf from Bowtie and output.vcf from BWA.

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