{SAMtools-version}_{dataset_id}_{sample_id}_stats.txt |
SAMtools stats sample level results |
{SAMtools-version}_{dataset_id}_{sample_id}-{library_id}_stats.txt |
SAMtools stats library level results |
{SAMtools-version}_{dataset_id}_{sample_id}-{library_id}-{rg_id}_stats.txt |
SAMtools stats readgroup level results |
{Picard-version}_{dataset_id}_{sample_id}_wgs-metrics.txt |
Picard CollectWgsMetrics results |
{Picard-version}_{dataset_id}_{sample_id}_hs-metrics.txt |
Picard CollectHsMetrics results |
{Qualimap-version}_{dataset_id}_{sample_id}_stats |
Directory of Qualimap results, including, genome_results.txt and either .pdf or .html and supporting directories |
{FastQC-version}_{dataset_id}_{sample_id}_fastqc |
Directory of sample level FastQC results |
{FastQC-version}_{dataset_id}_{sample_id}-{library_id}_fastqc |
Directory of library level FastQC results |
{FastQC-version}_{dataset_id}_{sample_id}-{library_id}-{rg_id}_fastqc |
Directory of readgroup level FastQC results |
{mosdepth-version}_{dataset_id}_{sample_id}-{window_size}.mosdepth.summary.txt |
mosdepth coverage results by region with a final line for total |
{mosdepth-version}_{dataset_id}_{sample_id}-{window_size}.mosdepth.global.dist.txt |
mosdepth coverage cumulative distribution indicating the proportion of total bases that were covered for at least a given coverage value |
{mosdepth-version}_{dataset_id}_{sample_id}-{window_size}.mosdepth.region.dist.txt |
mosdepth coverage cumulative distribution indicating the proportion of the windows that were covered for at least a given coverage value |
{mosdepth-version}_{dataset_id}_{sample_id}-{window_size}.regions.bed.gz |
mosdepth coverage bedfile giving coverage for each window |
{mosdepth-version}_{dataset_id}_{sample_id}-quantize-{q0}-{q1}-{q2}-{q3}.mosdepth.summary.txt |
mosdepth quantize coverage results by region with a final line for total |
{mosdepth-version}_{dataset_id}_{sample_id}-quantize-{q0}-{q1}-{q2}-{q3}.mosdepth.global.dist.txt |
mosdepth quantize cumulative distribution indicating the proportion of total bases that were covered for at least a given coverage value |
{mosdepth-version}_{dataset_id}_{sample_id}-quantize-{q0}-{q1}-{q2}-{q3}.quantized.bed.gz |
mosdepth quantize bed file |