output_dir |
Location where generated output should be saved. |
*target-with-enriched-off-target-intervals.bed |
New target file including original target intervals and intervals encompassing coverage-enriched off-target dbSNP sites. |
*target-with-enriched-off-target-intervals.bed.gz |
New compressed target file including original target intervals and intervals encompassing coverage-enriched off-target dbSNP sites. |
*off-target-dbSNP-depth-per-base.bed |
Per-base read depth at dbSNP loci outside of targeted regions. |
*collapsed_coverage.bed |
Per-base read depth at specified target intervals, collapsed by interval. (OPTIONAL) Set target_depth in config file. |
*target-depth-per-base.bed |
Per-base read depth at target intervals (not collapsed). (OPTIONAL) set save_raw_target_bed in config file. |
*genome-wide-dbSNP-depth-per-base.bed |
Per-base read depth at all dbSNP loci. (OPTIONAL) Set save_all_dbSNP in config file. |
*HsMetrics.txt |
QC output from CollectHsMetrics() |
.tsv,.bed |
Intermediate outputs of unformatted and unmerged depth files. (OPTIONAL) Set save_intermediate_files in config file. |
.interval_list |
Intermediate output of target bed file converted to picard's interval list format. (OPTIONAL) Set save_interval_list in config file. |
report.html, timeline.html and trace.txt |
A Nextflowreport, timeline and trace files |
log.command.* |
Process specific logging files created by nextflow. |