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| Code Block |
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cp bowtie/REL606.5.sam samtools/ cp bowtie/REL606.5.fasta samtools/ |
Index the reference file.
| Code Block |
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samtools faidx samtools/REL606.5.fasta |
Convert from SAM to BAM format.
| Code Block |
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samtools view -bS -o samtools/REL606.5.bam bowtie/REL606.5.sam |borderStyle=solid} |
Sort the BAM file.
| Code Block |
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samtools sort samtools/REL606.5.bam samtools/sorted_REL606.5 |
...
Output VCF file.
| Code Block |
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samtools mpileup -uf samtools/REL606.5.fasta samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> samtools/output.vcf |
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