1. ## step 1: Call candidate variants
    2. # 配对样本
    3. gatk Mutect2 \
    4.     -R ref.fasta \
    5.     -L intervals.interval_list \
    6.     -I tumor.bam -tumor tumor\
    7.     -I normal.bam -norma normal\
    8.     -germline-resource af-only-gnomad.vcf \
    9.     -pon panel_of_normals.vcf \
    10.     --f1r2-tar-gz f1r2.tar.gz \
    11.     -O unfiltered.vcf
    13. # 仅有肿瘤样本
    14. gatk Mutect2 \
    15.     -R ref.fasta \
    16.     -L intervals.interval_list \
    17.     -I tumor.bam -tumor tumor\
    18.     -germline-resource af-only-gnomad.vcf \
    19.     -pon panel_of_normals.vcf \
    20.     --f1r2-tar-gz f1r2.tar.gz \
    21.     -O unfiltered.vcf
    23. ## step 2: Calculate Contamination
    24. gatk GetPileupSummaries \
    25.     -I tumor.bam \
    26.     -V chr17_small_exac_common_3_grch38.vcf.gz \
    27.     -L chr17_small_exac_common_3_grch38.vcf.gz \
    28.     -O tumor.getpileupsummaries.table
    30. gatk GetPileupSummaries \
    31.     -I normal.bam \
    32.     -V chr17_small_exac_common_3_grch38.vcf.gz \
    33.     -L chr17_small_exac_common_3_grch38.vcf.gz \
    34.     -O normal.getpileupsummaries.table
    36. gatk CalculateContamination \
    37.     -I tumor.getpileupsummaries.table \
    38.     -matched normal.getpileupsummaries.table
    39.     -O calculatecontamination.table
    41. ## step 3: Learn Orientation Bias Artifacts
    42. gatk LearnReadOrientationModel \
    43.     -I f1r2.tar.gz \
    44.     -O read-orientation-model.tar.gz
    46. ## step 4: Filter Variants
    47. gatk FilterMutectCalls \
    48.     -V unfiltered.vcf \
    49.     --contamination-table calculatecontamination.table \
    50.     --ob-priors read-orientation-model.tar.gz \
    51.     -O filtered.vcf

    https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/

    https://www.jianshu.com/p/cfd72e478039

    https://www.jianshu.com/p/002daa39ded9