extdata-slash-HG001_GRCh38.table: Dataset HG001_GRCh38
In Hatoonli/vcfqc: What the Package Does (One Line, Title Case)

extdata/HG001_GRCh38.table

R Documentation

Dataset HG001_GRCh38

Description

A dataset containing GATK quality annotations for a VCF file generated using GATK Germline short variant discovery pipeline on HG001 reference sample from genome in a bottle project. This dataset is used as an example to display this package's functions

Format

A data frame with 4786095 rows and 12 variables:

CHROM: Chromosome
POS: Position
REF: Referenece
ALT: Alternative
FILTER: VQSR pass
QUAL: Quality
QD: QualByDepth
FS: FisherStrand
SOR: StrandOddsRatio
MQ: RMSMappingQuality
MQRankSum: MappingQualityRankSumTest
ReadPosRankSum: ReadPosRankSumTest

HG001_GRCh38.table

NA

Source

https://www.nist.gov/programs-projects/genome-bottle

Hatoonli/vcfqc documentation built on May 16, 2022, 12:19 p.m.

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