1000_Genomes_HighCov_chrY

• Versions: NYGC_30x_unphased

• Reference genome builds: GRCh38

• Type: hail.MatrixTable

Schema (NYGC_30x_unphased, GRCh38)

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Global fields:
    'metadata': struct {
        name: str,
        reference_genome: str,
        n_rows: int32,
        n_cols: int32,
        n_partitions: int32
    }
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Column fields:
    's': str
    'FamilyID': str
    'FatherID': str
    'MotherID': str
    'Sex': str
    'Population': str
    'Superpopulation': str
    'sample_qc': struct {
        dp_stats: struct {
            mean: float64,
            stdev: float64,
            min: float64,
            max: float64
        },
        gq_stats: struct {
            mean: float64,
            stdev: float64,
            min: float64,
            max: float64
        },
        call_rate: float64,
        n_called: int64,
        n_not_called: int64,
        n_filtered: int64,
        n_hom_ref: int64,
        n_het: int64,
        n_hom_var: int64,
        n_non_ref: int64,
        n_singleton: int64,
        n_snp: int64,
        n_insertion: int64,
        n_deletion: int64,
        n_transition: int64,
        n_transversion: int64,
        n_star: int64,
        r_ti_tv: float64,
        r_het_hom_var: float64,
        r_insertion_deletion: float64
    }
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Row fields:
    'locus': locus<GRCh38>
    'alleles': array<str>
    'rsid': str
    'qual': float64
    'filters': set<str>
    'info': struct {
        AC: int32,
        AF: float64,
        AN: int32,
        BaseQRankSum: float64,
        ClippingRankSum: float64,
        DP: int32,
        DS: bool,
        END: int32,
        ExcessHet: float64,
        FS: float64,
        HaplotypeScore: float64,
        InbreedingCoeff: float64,
        MLEAC: int32,
        MLEAF: float64,
        MQ: float64,
        MQ0: int32,
        MQRankSum: float64,
        NEGATIVE_TRAIN_SITE: bool,
        POSITIVE_TRAIN_SITE: bool,
        QD: float64,
        RAW_MQ: float64,
        ReadPosRankSum: float64,
        SOR: float64,
        VQSLOD: float64,
        VariantType: str,
        culprit: str,
        AN_EAS: int32,
        AN_AMR: int32,
        AN_EUR: int32,
        AN_AFR: int32,
        AN_SAS: int32,
        AN_EUR_unrel: int32,
        AN_EAS_unrel: int32,
        AN_AMR_unrel: int32,
        AN_SAS_unrel: int32,
        AN_AFR_unrel: int32,
        AC_EAS: int32,
        AC_AMR: int32,
        AC_EUR: int32,
        AC_AFR: int32,
        AC_SAS: int32,
        AC_EUR_unrel: int32,
        AC_EAS_unrel: int32,
        AC_AMR_unrel: int32,
        AC_SAS_unrel: int32,
        AC_AFR_unrel: int32,
        AF_EAS: float64,
        AF_AMR: float64,
        AF_EUR: float64,
        AF_AFR: float64,
        AF_SAS: float64,
        AF_EUR_unrel: float64,
        AF_EAS_unrel: float64,
        AF_AMR_unrel: float64,
        AF_SAS_unrel: float64,
        AF_AFR_unrel: float64
    }
    'a_index': int32
    'was_split': bool
    'variant_qc': struct {
        dp_stats: struct {
            mean: float64,
            stdev: float64,
            min: float64,
            max: float64
        },
        gq_stats: struct {
            mean: float64,
            stdev: float64,
            min: float64,
            max: float64
        },
        AC: array<int32>,
        AF: array<float64>,
        AN: int32,
        homozygote_count: array<int32>,
        call_rate: float64,
        n_called: int64,
        n_not_called: int64,
        n_filtered: int64,
        n_het: int64,
        n_non_ref: int64,
        het_freq_hwe: float64,
        p_value_hwe: float64
    }
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Entry fields:
    'AB': float64
    'AD': array<int32>
    'DP': int32
    'GQ': int32
    'GT': call
    'MIN_DP': int32
    'MQ0': int32
    'PGT': call
    'PID': str
    'PL': array<int32>
    'RGQ': int32
    'SB': array<int32>
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Column key: ['s']
Row key: ['locus', 'alleles']
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