Case flags in the CIP-API and Interpretation Portal¶

A case may have one or more of the following flags applied:

Flag	Description
`LOW_COVERAGE`	<95% of the autosomal genome covered at ≥15x calculated from reads with mapping quality >10 after filtering reads as described in Genome coverage. Samples with this quality flag will have >85x10^9 bases with quality ≥30, achieved from reads that are not duplicated and without double counting overlapping bases in the same fragment.
`SALIVA_SAMPLE`	Genome sequencing performed using DNA extracted from saliva. The increased risk of baceterial contamination in saliva samples can reduce genome sequencing quality, resulting in reduced quality associated with real genomic variants and/or an increased number of false positive variants detected.
`UNUSUAL_SEX_KARYOTYPE`	At least one member of the family has a sex karyotype that is not XX or XY.
`INCORRECT_OR_DISCORDANT_SEX_KARYOTYPE`	Reported karyotypic and phenotypic sex are discrepant but the karyotypic sex is supported by the sex inferred from the genomic data in at least one family member.
`INFERRED_GENETIC_AND_REPORTED_SEX_DISCORDANT`	Reported sex is discrepant from the inferred genetic sex and the Disorders of Sex development panel has been applied.
`UNKNOWN_PHENOTYPIC_SEX`	Phenotypic sex is unknown for at least one member of a family.
`POOR_QUALITY_CNV_CALLS`	Majority of CNV calls in the proband are expected to be of poor quality.
`SUSPECTED_POOR_QUALITY_CNV_CALLS`	An increased number of poor quality CNV calls is suspected.
`ddddddddd[mat\|pat]UPDnn[i\|h\|m][c\|p]`	Uniparental disomy detected that segregates with disease. Refer to uniparental disomy section for further details on interpretation of the details provided in this case flag.