vcf2df

vcf2df

Reads sample.vcf.gz and writes sample.parquet

Reserved column names:

• VARIANTKEY (STRING)

  Variantkey is CHR-POS-REF-ALT for small variants and CHR-POS-END-SVTYPE for structural variants. CHR without chr preffix.

• CHROM (STRING)

  Chromosome (including chr preffix).

• POS (INT)

  Position (1-based)

• REF (STRING)

  Reference allele. Empty for structural variants.

• ALT (STRING)

  Alternate allele. Empty for structural variants.

• QUAL (INT)

  Quality score (Integer)

• PASS (BOOL)

  Boolean describing filter == PASS || filter == "."

• IS_SV (BOOL)

  Boolean structural variant.",

• SVTYPE (STRING)

  Structural variant type (ex. DEL, DUP, INV, ...)

• END (INT)

  End position of variant (1-based).

• NUMALTS (INT)

  Number of alternate alleles (0, 1, 2)

• SAMPLE (STRING)

  Sample string.

• IS_PHASED (BOOL)

  Boolean if variant is phased.

• PHASE_ID (STRING)

  String identifying variant phase.

• REF_READS (INT)

  Read depth for ref.

• ALT_READS (INT)

  Read depth for alt.

Samples:

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.

Footer:

All columns are described in the parquet metadata (footer) key-values.