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    #samtools

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    #samtools sort

    #samtools faidx

    #permutation in r

    #aggregate in r

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    #merge multiple data frames in r

    #bowtie2 manual

    #fastx toolkit

    #fastqc

    #simple bioinformatics platform

    #bwa mem manual

    #bedtools intersect

    #sam to bam

    #convert sam to bam

    #samtools sam to bam

    #bcftools

    #vcf format

    #vcf file format

    #sam format

    #samtools flagstat

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