# Variant-wise QC metrics file Variant-wise QC metrics file is available to Sandbox users. **Sandbox directory** Variant-wise metrics file (and index file) are available in the following sandbox directory: ``` gs://finngen-production-library-green/imputation_panel/v4.2/variant_qc/sisu4.2_panel_var_wise_QC_metrics/ ``` To generate SISu v4.2 reference panel, sample-, genotype- and variant-wise quality control (QC) filtering procedures were applied by an iterative manner on the high-coverage WGS (hcWGS) data. Then, a allele count (AC) > 2 cutting off was applied, symmetrically. Variant-wise metrics were exported for monitoring data quality after major QC steps. We offer variant-wise QC metrics tsv files of Sisu v4.2 reference panel after major QC steps: raw data, after sample-wise QC data and after sample-, genotype- and variant-wise QC data, for autosomal chromosomes and chromosome X separately. **Variant-wise QC metrics file** | QC Steps | Autosomal chromosome | Chromosome X | | ------------------------------------------ | --------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Raw VCF data from WashU (w/ 10500 samples) | sisu4.2\_panel\_autosomal\_raw\_variant\_wise\_qc\_metrics.tsv.gz / .tbi | sisu4.2\_panel\_chrX\_raw\_variant\_wise\_qc\_metrics.tsv.gz | | After sample-wise QC (w/ 8554 samples) | sisu4.2\_panel\_autosomal\_after\_sample\_qc\_variant\_wise\_qc\_metrics.tsv.gz / .tbi | sisu4.2\_panel\_chrX\_after\_sample\_qc\_variant\_wise\_qc\_metrics.tsv.gz | | After genotype- and variant-wise QC | sisu4.2\_panel\_autosomal\_after\_sample\_genotype\_variant\_qc\_variant\_wise\_qc\_metrics.tsv.gz / .tbi | sisu4.2\_panel\_chrX\_XPAR\_after\_sample\_genotype\_variant\_qc\_variant\_wise\_qc\_metrics.tsv.gz; sisu4.2\_panel\_chrX\_nonXPAR\_after\_sample\_genotype\_variant\_qc\_variant\_wise\_qc\_metrics.tsv.gz | | After AC>2 filtering, symmetrically | | | **General description** Autosomal chromosomes variant-wise metrics file contains 24 columns: | Column Number | Name | Type | Description | | ------------- | --------------------- | --------------- | ------------------------------------------------------------------------------------------ | | 1 | #chr | int | Chromosome number (1-22) where the variant is located | | 2 | pos | int | Genomic position of the variant on the specified chromosome | | 3 | Variant | string | Variant identifier in the format "chromosome:position:reference\_allele:alternate\_allele" | | 4 | callRate | double | Fraction of samples with called genotypes | | 5 | AC | int | Count of alternate alleles | | 6 | AF | double | Calculated alternate allele frequency (q) | | 7 | nCalled | int | Sum of nHomRef, nHet, and nHomVar | | 8 | nNotCalled | int | Number of uncalled samples | | 9 | nHomRef | int | Number of homozygous reference samples | | 10 | nHet | int | Number of heterozygous samples | | 11 | nHomVar | int | Number of homozygous alternate samples | | 12 | dpMean | double | Depth mean across all samples | | 13 | dpStDev | double | Depth standard deviation across all samples | | 14 | gqMean | double | The average genotype quality across all samples | | 15 | dpStDev | double | Depth standard deviation across all samples | | 16 | nNonRef | int | Sum of nHet and nHomVar | | 17 | rHeterozygosity | double | Proportion of heterozygotes | | 18 | rHetHomVar | double | Ratio of heterozygotes to homozygous alternates | | 19 | rExpectedHetFrequency | double | Expected rHeterozygosity based on HWE | | 20 | pHWE | double | p-value from Hardy Weinberg Equilibrium null model | | 21 | FILTERS | list of strings | FILTER entry in the VCF, \[] means PASS | | 22 | QD | double | Quality by Depth (QD) of INFO field in the VCF | | 23 | IS\_INDEL | boolean | Insertion-deletion variant | | 24 | IS\_SNP | boolean | Single nucleotide variant | Chromosome X variant-wise metrics file contains 25 columns: | Column Number | Name | Type | Description | | ------------- | --------------------------------- | --------------- | --------------------------------------------------------------------------------------------------------------------------------------- | | 1 | locus | tlocus | Hail type for a genomic coordinate with a contig and a position, e.g., chrX:10009 | | 2 | alleles | tarray of tstr | Hail type for variable-length arrays of text strings, e.g., \["A","G"] | | 3 | filters | list of strings | FILTER entry in the VCF, \[] means PASS | | 4 | variant\_qc.dp\_stats.mean | float64 | Mean depth of coverage (DP) across samples. | | 5 | variant\_qc.dp\_stats.stdev | float64 | Standard deviation of depth of coverage (DP) across samples. | | 6 | variant\_qc.dp\_stats.min | int32 | Minimum depth of coverage (DP) across samples. | | 7 | variant\_qc.dp\_stats.max | int32 | Maximum depth of coverage (DP) across samples. | | 8 | variant\_qc.gq\_stats.mean | float64 | Mean genotype quality (GQ) across samples. | | 9 | variant\_qc.gq\_stats.stdev | float64 | Standard deviation of genotype quality (GQ) across samples. | | 10 | variant\_qc.gq\_stats.min | int32 | Minimum genotype quality (GQ) across samples. | | 11 | variant\_qc.gq\_stats.max | int32 | Maximum genotype quality (GQ) across samples. | | 12 | variant\_qc.AC | array\ | Calculated allele count, one element per allele, including the reference. Sums to AN. | | 13 | variant\_qc.AF | array\ | Calculated allele frequency, one element per allele, including the reference. Sums to one. Equivalent to AC / AN. | | 14 | variant\_qc.AN | int32 | Total number of called alleles. | | 15 | variant\_qc.homozygote\_count | array\ | Number of homozygotes per allele. One element per allele, including the reference. | | 16 | variant\_qc.call\_rate | float64 | Fraction of calls neither missing nor filtered. Equivalent to n\_called / count\_cols(). | | 17 | variant\_qc.n\_called | int64 | Number of samples with a defined GT. | | 18 | variant\_qc.n\_not\_called | int64 | Number of samples with a missing GT. | | 19 | variant\_qc.n\_filtered | int64 | Number of filtered entries. | | 20 | variant\_qc.n\_het | int64 | Number of heterozygous samples. | | 21 | variant\_qc.n\_non\_ref | int64 | Number of samples with at least one called non-reference allele. | | 22 | variant\_qc.het\_freq\_hwe | float64 | Expected frequency of heterozygous samples under Hardy-Weinberg equilibrium. See functions.hardy\_weinberg\_test() for details. | | 23 | variant\_qc.p\_value\_hwe | float64 | p-value from two-sided test of Hardy-Weinberg equilibrium. See functions.hardy\_weinberg\_test() for details. | | 24 | variant\_qc.p\_value\_excess\_het | float64 | p-value from one-sided test of Hardy-Weinberg equilibrium for excess heterozygosity. See functions.hardy\_weinberg\_test() for details. | | 25 | info.QD | double | Quality by Depth (QD) of INFO field in the VCF. |