Quality control on variant data.
stats List<AlignmentStats> | Alignment stats for each alignment file (BAM). See alignment stats data model schema. |
files List<File> | List of files related to the variant data, , e.g.: images. |
geneCoverageStats LIst<GeneCoverageStats>
| Gene coverage stats for each alignment file (BAM). fileId String | File ID. | sampleId String | Sample ID. | gene String | Gene name. | stats List<TranscriptCoverageStats> | id String | Transcript ID. | name String | Transcript name. | biotype String | Transcript biotype. | chromosome String | Chromosome where the transcript is located. | start int | Position where the transcript starts. | end int | Position where the transcript ends. | length int | The transcript length as the sum of the lengths of its exons. | depths Double[10] | % coverage for 1x, 5x, 10x, 15x, 20x, 25x, 30x, 40x, 50x, 60x, 75x and 100x | lowCoverageThreshold int | Regions under this coverage depth threshold will be reported in the list lowCoverageRegions. Default value: 30. | lowCoverageRegionStats List<LowCoverageRegionStats> | Statistics for regions whose coverage depth is under the value lowCoverageThreshold. chromosome String | Chromosome. | start int | Region start position. | end int | Region end position | depthAvg double | Average depth. | depthMin int | Minimum depth. |
| exonStats List<ExonCoverageStats> | Statistics for each exon in the transcript. id String | Exon ID. | chromosome String | Chromosome. | start int | Region start position. | end int | Region end position | depthAvg double | Average depth. | depthMin int | Minimum depth. | depthMax int | Maximum depth. |
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