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

0.15

maximum

1

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_paranoid_mode

Weaken weight of ‘criteria provided’ in variant assessment

When set, then variant assessments with and without assertion are interpreted as equally important. By default, they are not those with assessment override the others.

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

  • 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