JSON Schema

This section contains the JSON schemas used in the VarFish Server API.

Case Query Schema V1

varfish-server case query settings

https://raw.githubusercontent.com/bihealth/varfish-server/main/variants/schemas/case-query-v1.json
Single case query settings for varfish-server
type	object
properties
database	The transcript database to use
	You can select between either using refseq or ensembl transcripts, defaults to refseq
	type	string
	examples	refseq
		ensembl
	default	refseq
effects	The effects schema
	An explanation about the purpose of this instance.
	type	array
	examples	missense_variant
		stop_gained
		stop_lost
	default
	items	type	string
		enum	3_prime_UTR_exon_variant, 3_prime_UTR_intron_variant, 5_prime_UTR_exon_variant, 5_prime_UTR_intron_variant, coding_transcript_intron_variant, complex_substitution, direct_tandem_duplication, disruptive_inframe_deletion, disruptive_inframe_insertion, downstream_gene_variant, exon_loss_variant, feature_truncation, frameshift_elongation, frameshift_truncation, frameshift_variant, inframe_deletion, inframe_insertion, intergenic_variant, internal_feature_elongation, missense_variant, mnv, non_coding_transcript_exon_variant, non_coding_transcript_intron_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, start_lost, stop_gained, stop_lost, stop_retained_variant, structural_variant, synonymous_variant, transcript_ablation, upstream_gene_variant
	additionalItems	False
	uniqueItems	True
exac_enabled	Whether to enable ExAC frequency filter
	Set to true to enable ExAC frequency filter
	type	boolean
	examples	True
		False
	default	False
exac_frequency	anyOf	type	null
		Maximal allele frequency in ExAC
		When exac_enabled then only variants with at an allele frequency of exac_frequency or below will pass the filter, use null for not applying threshold
		type	number
		examples	0.05
		maximum	0.05
		minimum	0
exac_heterozygous	anyOf	type	null
		Maximal heterozygous state count in ExAC
		When exac_enabled then only variants with at most exac_heterozygous variants in heterozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		default	0
exac_homozygous	anyOf	type	null
		Maximal homozygous state count in ExAC
		When exac_enabled then only variants with at most exac_homozygous variants in homozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		default	0
exac_hemizygous	anyOf	type	null
		Maximal hemizygous state count in ExAC
		When exac_enabled then only variants with at most exac_hemizygous variants in hemizygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		minimum	0
gnomad_exomes_enabled	Whether to enable gnomAD exomes frequency filter
	Set to true to enable gnomAD exomes frequency filter
	type	boolean
	examples	True
		False
	default	False
gnomad_exomes_frequency	anyOf	type	null
		Maximal allele frequency in gnomAD exomes
		When gnomad_exomes_enabled then only variants with at an allele frequency of gnomad_exomes_frequency or below will pass the filter, use null for not applying threshold
		type	number
		examples	0.05
		maximum	0.05
		minimum	0
gnomad_exomes_heterozygous	anyOf	type	null
		Maximal heterozygous state count in gnomAD exomes
		When gnomad_exomes_enabled then only variants with at most gnomad_exomes_heterozygous variants in heterozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		default	0
gnomad_exomes_homozygous	anyOf	type	null
		Maximal homozygous state count in gnomAD exomes
		When gnomad_exomes_enabled then only variants with at most gnomad_exomes_homozygous variants in homozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		default	0
gnomad_exomes_hemizygous	anyOf	type	null
		Maximal hemizygous state count in gnomAD exomes
		When gnomad_exomes_enabled then only variants with at most gnomad_exomes_hemizygous variants in hemizygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		minimum	0
gnomad_genomes_enabled	Whether to enable gnomAD genomes frequency filter
	Set to true to enable gnomAD genomes frequency filter
	type	boolean
	examples	True
		False
	default	False
gnomad_genomes_frequency	anyOf	type	null
		Maximal allele frequency in gnomAD genomes
		When gnomad_genomes_enabled then only variants with at an allele frequency of gnomad_genomes_frequency or below will pass the filter, use null for not applying threshold
		type	number
		examples	0.05
		maximum	0.05
		minimum	0
gnomad_genomes_heterozygous	anyOf	type	null
		Maximal heterozygous state count in gnomAD genomes
		When gnomad_genomes_enabled then only variants with at most gnomad_genomes_heterozygous variants in heterozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		default	0
gnomad_genomes_homozygous	anyOf	type	null
		Maximal homozygous state count in gnomAD genomes
		When gnomad_genomes_enabled then only variants with at most gnomad_genomes_homozygous variants in homozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		default	0
gnomad_genomes_hemizygous	anyOf	type	null
		Maximal hemizygous state count in gnomAD genomes
		When gnomad_genomes_enabled then only variants with at most gnomad_genomes_hemizygous variants in hemizygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		minimum	0
thousand_genomes_enabled	Whether to enable thousand genomes frequency filter
	Set to true to enable thousand genomes frequency filter
	type	boolean
	examples	True
		False
	default	False
thousand_genomes_frequency	anyOf	type	null
		Maximal allele frequency in thousand genomes
		When thousand_genomes_enabled then only variants with at an allele frequency of thousand_genomes_frequency or below will pass the filter, use null for not applying threshold
		type	number
		examples	0.05
		maximum	0.05
		minimum	0
thousand_genomes_heterozygous	anyOf	type	null
		Maximal heterozygous state count in thousand genomes
		When thousand_genomes_enabled then only variants with at most thousand_genomes_heterozygous variants in heterozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		default	0
thousand_genomes_homozygous	anyOf	type	null
		Maximal homozygous state count in thousand genomes
		When thousand_genomes_enabled then only variants with at most thousand_genomes_homozygous variants in homozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		default	0
thousand_genomes_hemizygous	anyOf	type	null
		Maximal hemizygous state count in thousand genomes
		When thousand_genomes_enabled then only variants with at most thousand_genomes_hemizygous variants in hemizygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		minimum	0
inhouse_enabled	Whether to enable thousand genomes frequency filter
	Set to true to enable in-house frequency filter
	type	boolean
	examples	True
		False
	default	False
inhouse_carriers	anyOf	type	null
		Maximal carrier count in in-house database
		When inhouse_enabled then only variants with at most inhouse_carriers carriers in the in-house database will pass the filter, use null, for not applying threshold
		type	integer
		examples	20
		minimum	0
inhouse_heterozygous	anyOf	type	null
		Maximal heterozygous state count in thousand genomes
		When inhouse_enabled then only variants with at most inhouse_heterozygous variants in heterozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	10
		minimum	0
inhouse_homozygous	anyOf	type	null
		Maximal homozygous state count in thousand genomes
		When inhouse_enabled then only variants with at most inhouse_homozygous variants in homozygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	10
		minimum	0
inhouse_hemizygous	anyOf	type	null
		Maximal hemizygous state count in thousand genomes
		When inhouse_enabled then only variants with at most inhouse_hemizygous variants in hemizygous state will pass the filter, use null for not applying threshold
		type	integer
		examples	10
		minimum	0
mtdb_enabled	Whether to enable mtdb frequency filter
	Set to true to enable mtdb frequency filter
	type	boolean
	examples	True
		False
	default	False
mtdb_count	anyOf	type	null
		Maximal number/absolute frequency of carriers in mtdb
		When mtdb_enabled then only variants with at most mtdb_count carriers will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		minimum	0
mtdb_frequency	anyOf	type	null
		Maximal relative frequencey of carriers in mtdb
		When mtdb_enabled then only variants with a fraction (between 0 and 0.05) of at most mtdb_frequency, use null for not applying threshold
		type	number
		examples	0.05
		maximum	0.05
		minimum	0
helixmtdb_enabled	Whether to enable helixmtdb frequency filter
	Set to true to enable helixmtdb frequency filter
	type	boolean
	examples	True
		False
	default	False
helixmtdb_frequency	anyOf	type	null
		Maximal carrier frequency in helixmtdb
		When helixmtdb_enabled then only variants with at a carrier frequency of helixmtdb_frequency or below will pass the filter, use null for not applying threshold
		type	number
		examples	0.001
			0.05
		maximum	1
		minimum	0
helixmtdb_het_count	anyOf	type	null
		Maximal heteroplasmy frequency in helixmtdb
		When helixmtdb_enabled then only variants with at number of carriers in heteroplasmic state of helixmtdb_het_count or below will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		minimum	0
helixmtdb_hom_count	anyOf	type	null
		Maximal homoplasmy frequency in helixmtdb
		When helixmtdb_enabled then only variants with at number of carriers in homoplasmic state of helixmtdb_hom_count or below will pass the filter, use null for not applying threshold
		type	integer
		examples	1
			10
		minimum	0
mitomap_enabled	Whether to enable the mitomap carrier filter
	Set to true to enable mitomap carrier filter
	type	boolean
	examples	True
		False
	default	False
mitomap_count	anyOf	type	null
		Maximal number of carriers in mtDB
		When mitomap_enabled then only variants with at most mitomap_count carriers will pass the filter, use null for not applying threshold
		type	integer
		examples	10
		minimum	0
mitomap_frequency	anyOf	type	null
		The mitomap_frequency schema
		When mitomap_enabled then only variants with a relative frequency (between 0 and 1) will pass the filter, use null for not enabling threshold
		type	number
		examples	0.001
			0.05
		maximum	1
		minimum	0
transcripts_coding	Include variants on coding transcripts
	When enabled then variants whose most pathogenic effect is on a coding transcripts
	type	boolean
	examples	True
		False
	default	False
transcripts_noncoding	Include variants on non-coding transcripts
	When enabled then variants whose most pathogenic effect is on a non-coding transcripts
	type	boolean
	examples	True
		False
	default	True
var_type_snv	Include SNV variants
	When set to true then include singlenucleotide variants in the results
	type	boolean
	examples	True
		False
	default	True
var_type_indel	Include indel variants
	When set to true then include insertion and deletion variants (e.g., CGA>C and C>CGA) in the results
	type	boolean
	examples	True
		False
	default	True
var_type_mnv	Include MVN variants
	When set to true then include multinucleotide variants (e.g., CG>TT) in the results
	type	boolean
	examples	True
		False
	default	True
max_exon_dist	anyOf	type	null
		The largest distance to exons
		When set then only variants with at most max_exon_dist to the next exon are included, leave unset to not filter based on this
		type	integer
		examples	1
			10
		minimum	0
flag_simple_empty	Include variants marked with no flag
	When set (default) then variants that have no simple flag set are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_bookmarked	Include variants marked with “bookmarked” flag
	When set (default) then variants that have the “bookmarked” simple flag set are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_candidate	Include variants marked with “candidate” flag
	When set (default) then variants that have the “candidate” simple flag set are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_doesnt_segregate	Include variants marked with “does not segregate” flag
	When set (default) then variants that have the “does not segregate” simple flag set are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_final_causative	Include variants marked with “final causative” flag
	When set (default) then variants that have the “final causative” simple flag set are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_for_validation	Include variants marked with “for validation” flag
	When set (default) then variants that have the “for validation” simple flag set are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_no_disease_association	Include variants marked with “no disease association” flag
	When set (default) then variants that have the “no disease association” simple flag set are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_segregates	Include variants marked with “segregates” flag
	When set (default) then variants that have the “segregates” simple flag set are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_molecular_empty	Include variants that have the “molecular” flag unset
	When set (default) then variants that have the “molecular” flag unset are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_molecular_negative	Include variants marked with “molecular” flag set to “negative”
	When set (default) then variants that have the “molecular” flag set to “negative” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_molecular_positive	Include variants marked with “molecular” flag set to “positive”
	When set (default) then variants that have the “molecular” flag set to “positive” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_molecular_uncertain	Include variants marked with “molecular” flag set to “uncertain”
	When set (default) then variants that have the “molecular” flag set to “uncertain” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_phenotype_match_empty	Include variants that have the “phenotype match” flag unset
	When set (default) then variants that have the “phenotype match” flag unset are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_phenotype_match_negative	Include variants marked with “phenotype match” flag set to “negative”
	When set (default) then variants that have the “phenotype match” flag set to “negative” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_phenotype_match_positive	Include variants marked with “phenotype match” flag set to “positive”
	When set (default) then variants that have the “phenotype match” flag set to “positive” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_phenotype_match_uncertain	Include variants marked with “phenotype match” flag set to “uncertain”
	When set (default) then variants that have the “phenotype match” flag set to “uncertain” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_summary_empty	Include variants that have the “summary” flag unset
	When set (default) then variants that have the “summary” flag unset are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_summary_negative	Include variants marked with “summary” flag set to “negative”
	When set (default) then variants that have the “summary” flag set to “negative” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_summary_positive	Include variants marked with “summary” flag set to “positive”
	When set (default) then variants that have the “summary” flag set to “positive” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_summary_uncertain	Include variants marked with “summary” flag set to “uncertain”
	When set (default) then variants that have the “summary” flag set to “uncertain” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_validation_empty	Include variants that have the “validation” flag unset
	When set (default) then variants that have the “validation” flag unset are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_validation_negative	Include variants marked with “validation” flag set to “negative”
	When set (default) then variants that have the “validation” flag set to “negative” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_validation_positive	Include variants marked with “validation” flag set to “positive”
	When set (default) then variants that have the “validation” flag set to “positive” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_validation_uncertain	Include variants marked with “validation” flag set to “uncertain”
	When set (default) then variants that have the “validation” flag set to “uncertain” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_visual_empty	Include variants that have the “visual” flag unset
	When set (default) then variants that have the “visual” flag unset are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_visual_negative	Include variants marked with “visual” flag set to “negative”
	When set (default) then variants that have the “visual” flag set to “negative” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_visual_positive	Include variants marked with “visual” flag set to “positive”
	When set (default) then variants that have the “visual” flag set to “positive” are included in the result
	type	boolean
	examples	True
		False
	default	True
flag_visual_uncertain	Include variants marked with “visual” flag set to “uncertain”
	When set (default) then variants that have the “visual” flag set to “uncertain” are included in the result
	type	boolean
	examples	True
		False
	default	True
gene_allowlist	List of genes to restrict the resulting variants to
	List of gene symbols, entrez gene identifiers, or ENSEMBL gene identifiers to limit variants for (for a variant affecting multiple genes, the combinations of the variants and genes will be reported independently), leave empty to apply no such filter
	type	array
	examples	TTN
	default
	items	type	string
		pattern	^([a-zA-Z0-9_-]+)$
	additionalItems	True
gene_blocklist	List of genes to exclude from the result
	List of gene symbols, entrez gene identifiers, or ENSEMBL gene identifiers to exclude variants for (for a variant affecting multiple genes, the combinations of the variants and genes will be reported independently), leave empty to apply no such filter
	type	array
	examples	TTN
	default
	items	type	string
		pattern	^([a-zA-Z0-9_-]+)$
	additionalItems	True
remove_if_in_dbsnp	Remove variant if it exists in local copy dbSNP
	Set to true to exclude variants that are present in dbSNP from the result set
	type	boolean
	examples	True
		False
	default	False
require_in_clinvar	Restrict variants to those in local copy of Clinvar
	Set to true to restrict variants to those present in local copy of Clinvar
	type	boolean
	examples	True
		False
	default	False
clinvar_include_benign	Whether to include variants marked as benign in local Clinvar copy if ``require_in_clinvar``
	Set to true (default) to make variants pass the filter that are marked as benign in the local Clinvar copy, set to false to make them not pass the filter
	type	boolean
	examples	True
		False
	default	True
clinvar_include_pathogenic	Whether to include variants marked as pathogenic in local Clinvar copy if ``require_in_clinvar``
	Set to true (default) to make variants pass the filter that are marked as pathogenic in the local Clinvar copy, set to false to make them not pass the filter
	type	boolean
	examples	True
		False
	default	True
clinvar_include_likely_benign	Whether to include variants marked as likely benign in local Clinvar copy if ``require_in_clinvar``
	Set to true (default) to make variants pass the filter that are marked as likely benign in the local Clinvar copy, set to false to make them not pass the filter
	type	boolean
	examples	True
		False
	default	True
clinvar_include_likely_pathogenic	Whether to include variants marked as likely pathogenic in local Clinvar copy if ``require_in_clinvar``
	Set to true (default) to make variants pass the filter that are marked as likely pathogenic in the local Clinvar copy, set to false to make them not pass the filter
	type	boolean
	examples	True
		False
	default	True
clinvar_include_uncertain_significance	Whether to include variants marked as unknown certificance in local Clinvar copy if ``require_in_clinvar``
	Set to true (default) to make variants pass the filter that are marked as of unknown significance in the local Clinvar copy, set to false to make them not pass the filter
	type	boolean
	examples	True
		False
	default	True
genomic_region	List of genomic regions to limit the query to
	When set thenonly variants contained in or overlapping with the given genomic regions pass the filter, leave empty to apply no region filter
	type	array
	examples	chr1:100,000,00-110,00,00
		chrY
		X
		Y
	default
	items	type	string
		pattern	^[a-zA-Z0-9]+(:(\d+(,\d+)*)-(\d+(,\d+)*))?$
patho_enabled	Enable pathogenicity annotation
	Set to true to enable annotation with pathogenicity, requires setting a value for patho_score
	type	boolean
	examples	True
		False
	default	False
patho_score	anyOf	type	null
		The pathogenicity score to use for annotating variants
		Select pathogenicity score to use if patho_enabled. Must be one of the pathogenicity scores enabled in the VarFish server instance (depends on the installation)
		type	string
		examples	cadd
			mutationtaster
prio_enabled	Enable phenotype-based prioritization of variants
	Select
	type	boolean
	examples	True
		False
	default	False
prio_algorithm	anyOf	type	null
		The phenotype-based prioritization algorithm to use for priorizing variants
		Select algorithm to use if prio_enabled. Must be one of the algorithms enabled in the VarFish server instance (depends on the installation)
		type	string
		examples	phenix
			hiphive
			hiphive-human
			hiphive-mouse
prio_hpo_terms	anyOf	type	null
		The prio_hpo_terms schema
		An explanation about the purpose of this instance.
		type	array
		examples
		default
		items	type	string
			pattern	HP:\d+
		additionalItems	True
require_in_hgmd_public	The require_in_hgmd_public schema
	An explanation about the purpose of this instance.
	type	boolean
	examples	False
	default	False
recessive_mode	anyOf	type	null
		Enable and select the biallelic recessive inheritance filter
		Use “compound-recessive” to restrict to variants compatible with compound recessive mode of inheritance and “recessive” to restrict to compatibility with either compound and homozygous recessive mode of inheritance. Use recessive_index to select the index for recessive inheritance
		type	string
		enum	recessive, compound-recessive
recessive_index	anyOf	type	null
		Select the recessive index
		Set to the identifier of the recessive index
		type	string
		examples	CHILD-NAME
denovo_index	anyOf	type	null
		Select the denovo index
		Set to the identifier of the de novo index
		type	string
		examples	CHILD-NAME
quality	Quality filter threshold
	Set quality thresholds for each individual. The key are the individual names and the values follows the defined schema from below
	type	object
	examples	SAMPLE	dp_het	10
			dp_hom	5
			ab	0.3
			gq	20
			ad	3
			ad_max	200
			fail	drop-variant
		FATHER	gq	40
			fail	ignore
		MOTHER	gq	40
			fail	ignore
		CHILD	gq	40
			fail	drop-variant
	patternProperties
	.*	type	object
		properties
		dp_het	Minimal total depth of coverage for heterozygous variants
			If set then exclude variants with lower total depth of coverage in sample’s genotype call for heterozygous variants
			type	integer
			minimum	0
			default	0
		dp_hom	Minimal total depth coverage for homozygous and hemizygous variants
			If set then exclude variants with lower total depth of coverage in sample’s genotype call for homozygous variants
			type	integer
			minimum	0
			default	0
		ab	Minimal allelic balance for heterozygous variants
			If set then exclude variants with lower allelic balance in sample’s genotype call
			type	number
			maximum	1
			minimum	0
			default	0
		gq	Minimal genotype call quality
			If set then exclude variants with lower genotype quality in sample’s genotype call
			type	integer
			minimum	0
			default	0
		ad	Minimal number of read in alternative allele
			If set then exclude variants with lower depth of coverage on alternate allele in sample’s genotype call
			type	integer
			minimum	0
			default	0
		ad_max	anyOf	type	null
				Maximal alternate allele depth of coverage
				If set then exclude variants with higher depth of coverage on alternate allele in sample’s genotype call
				type	integer
				minimum	0
		fail	Action to perform when genotype filter threshold is not passed
			Actions: ignore: ignore failure, drop-variant: drop whole variant (if ONE genotype in the variant fails filter), no-call: interpret as no-call
			type	string
			enum	ignore, drop-variant, no-call
			default	ignore
		additionalProperties	False
genotype	Genotype filter settings
	Set genotype filter for each individual, must be given for each individual in query with genotype data
	type	object
	examples	SAMPLE	hom
		FATHER	ref
		MOTHER	ref
		CHILD	het
	patternProperties
	.*	anyOf	type	null
			type	string
			enum	any, ref, het, hom, non-hom, variant, non-variant, non-reference
additionalProperties	False

Case QC Schema V1

varfish-server case QC info

https://raw.githubusercontent.com/bihealth/varfish-server/main/importer/schemas/case-qc-v1.json
Per case quality control information for varfish
type	object
patternProperties
.*	type	object
	properties
	bamstats	type	object
		properties
		raw total sequences	raw total sequences
			type	integer
			minimum	0
		filtered sequences	filtered sequences
			type	integer
			minimum	0
		sequences	sequences
			type	integer
			minimum	0
		is sorted	is sorted
			type	integer
			minimum	0
		1st fragments	1st fragments
			type	integer
			minimum	0
		last fragments	last fragments
			type	integer
			minimum	0
		reads mapped	reads mapped
			type	integer
			minimum	0
		reads mapped and paired	reads mapped and paired
			type	integer
			minimum	0
		reads unmapped	reads unmapped
			type	integer
			minimum	0
		reads properly paired	reads properly paired
			type	integer
			minimum	0
		reads paired	reads paired
			type	integer
			minimum	0
		reads duplicated	reads duplicated
			type	integer
			minimum	0
		reads MQ0	reads MQ0
			type	integer
			minimum	0
		reads QC failed	reads QC failed
			type	integer
			minimum	0
		non-primary alignments	non-primary alignments
			type	integer
			minimum	0
		total length	total length
			type	integer
			minimum	0
		total first fragment length	total first fragment length
			type	integer
			minimum	0
		total last fragment length	total last fragment length
			type	integer
			minimum	0
		bases mapped	bases mapped
			type	integer
			minimum	0
		bases mapped (cigar)	bases mapped (cigar)
			type	integer
			minimum	0
bases trimmed		bases trimmed
		type	integer
	minimum	0
bases duplicated	bases duplicated
	type	integer
	minimum	0
mismatches	mismatches
	type	integer
	minimum	0
error rate	error rate
	error rate as fractions of 1
	type	number
	maximum	1
	minimum	0
average length	average length
	type	number
	minimum	0
average first fragment length	average first fragment length
	type	number
	minimum	0
average last fragment length	average last fragment length
	type	number
	minimum	0
maximum length	maximum length
	type	integer
	minimum	0
maximum first fragment length	maximum first fragment length
	type	integer
	minimum	0
maximum last fragment length	maximum last fragment length
	type	integer
	minimum	0
average quality	average quality
	type	number
	minimum	0
insert size average	insert size average
	type	number
	minimum	0
insert size standard deviation	insert size standard deviation
	type	number
	minimum	0
inward oriented pairs	inward oriented pairs
	type	integer
	minimum	0
outward oriented pairs	outward oriented pairs
	type	integer
	minimum	0
pairs with other orientation	pairs with other orientation
	type	integer
	minimum	0
pairs on different chromosomes	pairs on different chromosomes
	type	integer
	minimum	0
percentage of properly paired reads (%)	percentage of properly paired reads (%)
	type	number
	maximum	100
	minimum	0
min_cov_target	Minimal coverage percentage, counted per target
	Considering all targets, histogram of distribution regarding “minimal coverage of…”, the smallest coverage on a target makes the whole target count at that value
	type	object
	patternProperties
	\d+	Minimal coverage value histogram entry
		type	number
		examples	100
			99.9
			0
		maximum	100
		minimum	0
	additionalProperties	False
min_cov_base	Minimal coverage percentage, counted per base
	Considering all target bases, histogram of distribution regarding “minimal coverage of…”
	type	object
	patternProperties
	\d+	Minimal coverage value histogram entry
		type	number
		examples	100
			99.9
			0
		maximum	100
		minimum	0
	additionalProperties	False
summary	Coverage summary
	type	object
	properties
	mean coverage	Mean on-target coverage
		type	number
		examples	0
			100
		minimum	0
	target count	Total number of targets
		type	integer
		examples	0
			100
		minimum	0
	total target size	Total target size in bp
		type	integer
		examples	0
			100
		minimum	0
	additionalProperties	False
idxstats	type	object
	patternProperties
	.*	Read count for each chromosome
		type	object
		properties
		mapped	Mapped read count
			Number of mapped read on chromosome
			type	integer
			examples	0
				100
			minimum	0
		unmapped	Unmapped read count
			Number of unmapped read on chromosome (usually the mate maps)
			type	integer
			examples	0
				100
			minimum	0
		additionalProperties	False