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