├── README.md ├── add-on └── sam_bam.md ├── data └── SNV │ ├── adapters.fa │ ├── b37_cosmic_v70_140903.vcf.gz │ ├── b37_cosmic_v70_140903.vcf.gz.tbi │ ├── dbSnp-137_chr9.vcf.gz │ └── raw_reads │ ├── normal │ ├── run62DPDAAXX_8 │ │ ├── normal.64.pair1.fastq.gz │ │ └── normal.64.pair2.fastq.gz │ ├── run62DVGAAXX_1 │ │ ├── normal.64.pair1.fastq.gz │ │ └── normal.64.pair2.fastq.gz │ ├── run62MK3AAXX_5 │ │ ├── normal.64.pair1.fastq.gz │ │ └── normal.64.pair2.fastq.gz │ ├── runA81DF6ABXX_1 │ │ ├── normal.64.pair1.fastq.gz │ │ └── normal.64.pair2.fastq.gz │ ├── runA81DF6ABXX_2 │ │ ├── normal.64.pair1.fastq.gz │ │ └── normal.64.pair2.fastq.gz │ ├── runBC04D4ACXX_2 │ │ ├── normal.64.pair1.fastq.gz │ │ └── normal.64.pair2.fastq.gz │ ├── runBC04D4ACXX_3 │ │ ├── normal.64.pair1.fastq.gz │ │ └── normal.64.pair2.fastq.gz │ ├── runBD06UFACXX_4 │ │ ├── normal.64.pair1.fastq.gz │ │ └── normal.64.pair2.fastq.gz │ └── runBD06UFACXX_5 │ │ ├── normal.64.pair1.fastq.gz │ │ └── normal.64.pair2.fastq.gz │ └── tumor │ ├── run62DU0AAXX_8 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62DU6AAXX_8 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62DUUAAXX_8 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62DUYAAXX_7 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62DVMAAXX_4 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62DVMAAXX_5 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62DVMAAXX_6 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62DVMAAXX_7 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62DVMAAXX_8 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62JREAAXX_3 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62JREAAXX_4 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62JREAAXX_5 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62JREAAXX_6 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62JREAAXX_7 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── run62JREAAXX_8 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── runAC0756ACXX_4 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── runAC0756ACXX_5 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ ├── runAD08C1ACXX_1 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz │ └── runBD08K8ACXX_1 │ ├── tumor.64.pair1.fastq.gz │ └── tumor.64.pair2.fastq.gz ├── for_pdf ├── EBI_cancerGenmicsSNV_practical2016.pdf ├── EBI_cancer_workshop_SNV.pdf ├── README.md ├── all.md └── img │ ├── SV.png │ ├── ascii_table.png │ ├── base_qual_value.png │ ├── dn.png │ ├── doc.png │ ├── igv.png │ ├── mugqic_bfx.png │ ├── per.png │ ├── phred_formula.jpg │ ├── phred_formula.png │ ├── snv_call.png │ └── sr.png ├── img ├── SV.png ├── ascii_table.png ├── base_qual_value.png ├── dn.png ├── doc.png ├── igv.png ├── mugqic_bfx.png ├── per.png ├── phred_formula.jpg ├── phred_formula.png ├── snv_call.png └── sr.png ├── notes ├── _DOC.md ├── _DOC2.md ├── _fastqQC1.md ├── _markdup1.md ├── _merge1.md ├── _mpileup1.md ├── _trimmomatic.md └── _vcf1.md ├── scripts └── commands.sh └── solutions ├── _Conpair.md ├── _DOC1.md ├── _adapter1.md ├── _aln1.md ├── _aln2.md ├── _aln3.md ├── _aln4.md ├── _alnMetrics1.md ├── _conta.md ├── _data.md ├── _fastq1.md ├── _fastq2.md ├── _fastq3.md ├── _fastqQC1.md ├── _fastqQC2.md ├── _igv1.md ├── _insert1.md ├── _insert2.md ├── _markdup1.md ├── _markdup2.md ├── _markdup3.md ├── _markdup4.md ├── _markdup5.md ├── _merge1.md ├── _merge2.md ├── _realign1.md ├── _realign2.md ├── _realign3.md ├── _realign4.md ├── _recal1.md ├── _sambam1.md ├── _sambam2.md ├── _sambam3.md ├── _sambam4.md ├── _snpEff3.md ├── _snpEff4.md ├── _snpEff5.md ├── _snpeff1.md ├── _snpeff2.md ├── _trim1.md ├── _trim2.md ├── _trim3.md └── _vcf1.md /README.md: 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