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<int32>	Calculated allele count, one element per allele, including the reference. Sums to AN.
13	variant_qc.AF	array<float64>	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<int32>	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.