21 lines
561 B
Bash
Executable File
21 lines
561 B
Bash
Executable File
#!/bin/tcsh
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setenv refroot ~/work/refmut/
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setenv refname test2
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setenv ref "${refroot}/${refname}"
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setenv cov 100
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setenv sites 1
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setenv x '' # '-x 6696745:6708910'
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# testing samtools
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./SimulateReads.py --ref ${ref}.fasta --coverage ${cov} -n ${sites} -l 10 -t None ${x}
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# running samtools
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samtools import ${refname}__mut.None_10.bp_nsites.${sites}_cov.${cov}.ref ${refname}__mut.None_10.bp_nsites.${sites}_cov.${cov}.sam samtest.bam
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samtools sort samtest.bam samtestSorted
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samtools index samtestSorted.bam
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samtools pileup -f ${ref}.fasta samtestSorted.bam
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