Reads sample.vcf.gz and writes sample.parquet
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VARIANTKEY (STRING)
Variantkey is CHR-POS-REF-ALT for small variants and CHR-POS-END-SVTYPE for structural variants. CHR without chr preffix.
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CHROM (STRING)
Chromosome (including chr preffix).
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POS (INT)
Position (1-based)
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REF (STRING)
Reference allele. Empty for structural variants.
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ALT (STRING)
Alternate allele. Empty for structural variants.
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QUAL (INT)
Quality score (Integer)
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PASS (BOOL)
Boolean describing filter == PASS || filter == "."
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IS_SV (BOOL)
Boolean structural variant.",
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SVTYPE (STRING)
Structural variant type (ex. DEL, DUP, INV, ...)
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END (INT)
End position of variant (1-based).
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NUMALTS (INT)
Number of alternate alleles (0, 1, 2)
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SAMPLE (STRING)
Sample string.
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IS_PHASED (BOOL)
Boolean if variant is phased.
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PHASE_ID (STRING)
String identifying variant phase.
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REF_READS (INT)
Read depth for ref.
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ALT_READS (INT)
Read depth for alt.
If vcf has 1+ sample genotypes, the parquet file will contain 1 line per sample with > 0 alleles. If the vcf does not contain samples, all variants will be represented in the parquet file.
All columns are described in the parquet metadata (footer) key-values.