These are the outputs of the SingleSampleQc.wdl workflow.
These outputs are the products of running tools in the workflow.
| Name | Source Tool | Notes |
|---|---|---|
validation_report |
Picard ValidateSamFile | |
alignment_summary_metrics_file |
Picard CollectAlignmentSummaryMetrics | |
bait_bias_detail_metrics |
Picard CollectSequencingArtifactMetrics | |
bait_bias_summary_metrics |
Picard CollectSequencingArtifactMetrics | |
gc_bias_detail_metrics |
Picard CollectGcBiasMetrics | |
gc_bias_pdf |
Picard CollectGcBiasMetrics | |
gc_bias_summary_metrics |
Picard CollectGcBiasMetrics | |
insert_size_histograph_pdf |
Picard CollectInsertSizeMetrics | |
insert_size_metrics_file |
Picard CollectInsertSizeMetrics | |
pre_adapter_detail_metrics |
Picard CollectSequencingArtifactMetrics | |
pre_adapter_summary_metrics |
Picard CollectSequencingArtifactMetrics | |
quality_distribution_pdf |
Picard QualityScoreDistribution | |
quality_distribution_metrics |
Picard QualityScoreDistribution | |
error_summary_metrics |
Picard CollectSequencingArtifactMetrics | |
selfSM |
VerifyBamId | |
duplication_metrics_file |
Picard CollectDuplicateMetrics | |
quality_yield_metrics |
Picard CollectQualityYieldMetrics | |
raw_wgs_metrics |
Picard CollectWgsMetrics | (WGS only) |
hs_metrics |
Picard CollectHsMetrics | (exome only) |
input_bam_md5 |
md5sum | |
input_bam_index |
samtools index | |
input_bam_idxstats |
samtools idxstats | |
input_bam_rx_result |
RxIdentifier | (tool implemented in this workflow) |
evaluated_metrics_File |
EvaluateMetrics | (tool implemented in this workflow) |
The workflow parses the above output files to additionally yield WDL outputs of certain values directly. (When this workflow is run in Terra, these values can be output directly into a datatable.)
| Name | Description | Purpose | Source Tool |
|---|---|---|---|
pct_chimeras |
% Chimeras | Variant detection | Picard CollectAlignmentSummaryMetrics |
read1_pf_mismatch_rate |
Read1 base mismatch rate | Sequence quality | Picard CollectAlignmentSummaryMetrics |
read2_pf_mismatch_rate |
Read2 base mismatch rate | Sequence quality | Picard CollectAlignmentSummaryMetrics |
median_insert_size |
Library insert size median | Batch characteristics | Picard CollectInsertSizeMetrics |
median_absolute_deviation |
Library insert size mad | Batch characteristics | Picard CollectInsertSizeMetrics |
contamination |
FREEMIX | Sample contamination | VerifyBamId |
percent_duplication |
% Duplication | Picard CollectDuplicateMetrics | |
q20_bases |
Total bases with Q20 or higher | Sequence quality | Picard CollectQualityYieldMetrics |
pf_q20_bases |
Picard CollectQualityYieldMetrics | ||
q30_bases |
Total bases with Q30 or higher | Sequence quality | Picard CollectQualityYieldMetrics |
pf_q30_bases |
Picard CollectQualityYieldMetrics | ||
mean_coverage |
Haploid coverage (WGS only) | Coverage depth | Picard CollectWgsMetrics |
pct_10x |
% coverage at 10X (WGS only) | Coverage breadth | Picard CollectWgsMetrics |
pct_20x |
% coverage at 20X (WGS only) | Coverage breadth | Picard CollectWgsMetrics |
pct_30x |
% coverage at 30X (WGS only) | Coverage breadth | Picard CollectWgsMetrics |
mean_target_coverage |
Coverage of the target regions (exome only) | Coverage depth | Picard CollectHsMetrics |
pct_target_bases_10x |
% target coverage at 10x (exome only) | Coverage breadth | Picard CollectHsMetrics |
pct_target_bases_20x |
% target coverage at 20x (exome only) | Coverage breadth | Picard CollectHsMetrics |
pct_target_bases_30x |
% target coverage at 30x (exome only) | Coverage breadth | Picard CollectHsMetrics |
input_bam_md5_hash |
MD5sum of the input BAM/CRAM file | Data integrity | md5sum |
input_bam_rx_value |
Estimated sex from evaluating the Rx | Sex estimation | RxIdentifier (implemented in workflow) |
evaluated_metrics |
Map data structure of which metrics pass and fail from the thresholds | Metric evaluation | EvaluateMetrics (implemented in workflow) |
overall_evaluation |
PASS/FAIL status for the sample | Quality control | EvaluateMetrics (implemented in workflow) |