Terminologies & Concepts

High quality reads

High quality reads refers to sequencing instrument filter. For Illumina sequencer, leverages internal quality filtering procedure called chastity filter. Reads that pass this filter are called "PF" for "pass-filter"

Primary alignments

Primary alignments refers to SAM Format Specification v1, section 1.2 ”Terminologies and Concepts”, “Multiple mapping“ & section 1.4 “The alignment section: mandatory fields”, “FLAG: Combination of bitwise FLAGs”

Base quality score

Base quality score refers to SAM Format Specification v1, section 1.4: “The alignment section: mandatory fields”, “QUAL”

Mapping quality

Mapping qualityscore refers to SAM Format Specification v1, section 1.4 “The alignment section: mandatory fields”, “MAPQ: MAPping Quality”

Phred scale

PHRED scale refers to SAM Format Specification v1, section 1.2 ”Terminologies and Concepts”, “Phred scale“

Duplicated reads

Duplicated reads refers to SAM Format Specification v1, section 1.4: “The alignment section: mandatory fields”, “FLAG: Combination of bitwise FLAGs”

Clipped bases

Clipped bases refers to SAM Format Specification v1, section 1.2: ”Terminologies and Concepts”, “Linear alignment“ & section 1.4 “The alignment section: mandatory fields”, “CIGAR: CIGAR string”

Picard CollectQualityYieldMetrics

Picard CollectQualityYieldMetrics refers to GATK documentation, section "CollectQualityYieldMetrics (Picard)" & GATK specifications

Picard CollectWgsMetrics

Picard CollectWgsMetrics refers to GATK documentation, section "CollectWgsMetrics (Picard)" & GATK specifications

Autosomes non gap regions

Autosomes non gap regions refers to the selection of chromosome 1 to 22, excluding chromosome X, Y, M and alternative contigs. In addition, gap regions as defined by UCSC are excluded. See NPM-sample-qc documentation

GRCh38 assembly

GRCh38 assembly refers to 1000genome-dragen-3.7.6 reference

Overlapping bases

Overlapping bases refers to mosdepth documentation, section "how it works"

High quality variants

High quality variants (PASS FILTER) refers to VCF Format Specicification v4.2, section 1.4.1 "FILTER - filter status:" & GATK generic hard-filtering recommendations