Recommended information for reporting sample sequencing details
| Attribute . | Attribute type . | Description . |
|---|---|---|
| Unique sample identifier | Identifier | The unique identifier for the sample |
| Component | Sample metadata | Category of sample type referring to experimental design (eg, tumor, normal, cell-free) |
| Tissue preservation | Sample metadata | Category of preservation method for tissue/sample (eg, frozen, FFPE) |
| Sequencing assay type | Assay metadata | Generic name for the assay used to generate the data (eg, WGS, WES) |
| Sequencing platform | Assay metadata | Unambiguous name of sequencing platforms used to generate the data for the sample |
| Target capture regions URL | Assay metadata | Link to a BED format file that specifies the regions targeted for sequencing (when applicable)∗ |
| Aligner | Analysis metadata | Generic name for the workflow/software used to generate alignments (eg, bwa-mem, minimap2) |
| Genomic reference | Analysis metadata | Exact version of the human genome reference used in the alignment of reads |
| Genomic reference URL | Analysis metadata | Link to human genome sequence. URL |
| Average insert size | Quality metric | Average insert size collected from samtools. Integer |
| Average read length | Quality metric | Average read length collected from samtools. Integer |
| MeanCorrectedCoverage | Quality metric | Mean coverage of whole genome or targeted regions, correcting for overlapping regions of reads, collected from Picard. Number |
| Pairs on diff chromosome | Quality metric | Pairs on different chromosomes collected from samtools. Integer |
| Total reads | Quality metric | Total number of reads per sample. Integer |
| Total uniquely mapped | Quality metric | Number of reads that map to genome. Integer |
| Total unmapped reads | Quality metric | Number of reads that did not map to genome. Integer |
| Proportion reads duplicated | Quality metric | Proportion of duplicated reads collected from samtools. Number |
| Proportion reads mapped | Quality metric | Proportion of mapped reads collected from samtools. Number |
| Proportion targets no coverage | Quality metric | Proportion of targets that did not reach 1× coverage over any base. Number∗ |
| Proportion coverage 10× | Quality metric | Proportion of all reference bases for WGS or targeted bases that achieves 10× or greater coverage |
| Proportion coverage 30× | Quality metric | Proportion of all reference bases for WGS or targeted bases that achieves 30× or greater coverage |
| Proportion coverage 100× | Quality metric | Proportion of all reference bases for WGS or targeted bases that achieves 100× or greater coverage∗ |
| Attribute . | Attribute type . | Description . |
|---|---|---|
| Unique sample identifier | Identifier | The unique identifier for the sample |
| Component | Sample metadata | Category of sample type referring to experimental design (eg, tumor, normal, cell-free) |
| Tissue preservation | Sample metadata | Category of preservation method for tissue/sample (eg, frozen, FFPE) |
| Sequencing assay type | Assay metadata | Generic name for the assay used to generate the data (eg, WGS, WES) |
| Sequencing platform | Assay metadata | Unambiguous name of sequencing platforms used to generate the data for the sample |
| Target capture regions URL | Assay metadata | Link to a BED format file that specifies the regions targeted for sequencing (when applicable)∗ |
| Aligner | Analysis metadata | Generic name for the workflow/software used to generate alignments (eg, bwa-mem, minimap2) |
| Genomic reference | Analysis metadata | Exact version of the human genome reference used in the alignment of reads |
| Genomic reference URL | Analysis metadata | Link to human genome sequence. URL |
| Average insert size | Quality metric | Average insert size collected from samtools. Integer |
| Average read length | Quality metric | Average read length collected from samtools. Integer |
| MeanCorrectedCoverage | Quality metric | Mean coverage of whole genome or targeted regions, correcting for overlapping regions of reads, collected from Picard. Number |
| Pairs on diff chromosome | Quality metric | Pairs on different chromosomes collected from samtools. Integer |
| Total reads | Quality metric | Total number of reads per sample. Integer |
| Total uniquely mapped | Quality metric | Number of reads that map to genome. Integer |
| Total unmapped reads | Quality metric | Number of reads that did not map to genome. Integer |
| Proportion reads duplicated | Quality metric | Proportion of duplicated reads collected from samtools. Number |
| Proportion reads mapped | Quality metric | Proportion of mapped reads collected from samtools. Number |
| Proportion targets no coverage | Quality metric | Proportion of targets that did not reach 1× coverage over any base. Number∗ |
| Proportion coverage 10× | Quality metric | Proportion of all reference bases for WGS or targeted bases that achieves 10× or greater coverage |
| Proportion coverage 30× | Quality metric | Proportion of all reference bases for WGS or targeted bases that achieves 30× or greater coverage |
| Proportion coverage 100× | Quality metric | Proportion of all reference bases for WGS or targeted bases that achieves 100× or greater coverage∗ |
All fields are recommended for WGS and targeted sequencing experiments with the exception of those marked with an asterisk, which are required only for targeted sequencing.