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Setup output directory.
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mkdir bowtie_samtools
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If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.
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cp bowtie/REL606.5.sam bowtie_samtools/ cp bowtie/REL606.5.fasta bowtie_samtools/ |
Index the reference file.
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samtools faidx bowtie_samtools/REL606.5.fasta
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Convert from SAM to BAM format.
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samtools view -bS -o bowtie_samtools/REL606.5.bam bowtie/REL606.5.sam |borderStyle=solid}
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Sort the BAM file.
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samtools sort bowtie_samtools/REL606.5.bam bowtie_samtools/sorted_REL606.5 |
Output VCF file.
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samtools mpileup -uf bowtie_samtools/REL606.5.fasta bowtie_samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> bowtie_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.
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