If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
IntervalListTools UNION corner case: doesn't keep all name fields if merged coordinates are same
When IntervalListTools UNION encounters two records with identical coordinates but different name fields, it outputs a single record with only one of the original name fields. E.g.
chr1 2228866 2228866 + NM_003036.3(SKI):c.100G>A chr1 2228866 2228866 + NM_003036.3(SKI):c.100G>T
chr1 2228866 2228866 + NM_003036.3(SKI):c.100G>A
whereas this is expected:
chr1 2228866 2228866 + NM_003036.3(SKI):c.100G>A|NM_003036.3(SKI):c.100G>T
The expected, name-concatenating, behavior works when the coordinates to be merged are not identical:
chr1 11992659 11992659 + NM_014874.3(MFN2):c.280C>T chr1 11992660 11992660 + NM_014874.3(MFN2):c.281G>A
chr1 11992659 11992660 + NM_014874.3(MFN2):c.280C>T|NM_014874.3(MFN2):c.281G>A
GATK command used:
java -jar $HOME/apps/GATK4.jar IntervalListTools \ --ACTION UNION \ -I /mnt/hdd/resources/clinvar/clinvar_2019-01-17/tab_delimited/clinvar_2019-01-17_variant_summary.pathogenic.tmp.interval_list \ -O /mnt/hdd/resources/clinvar/clinvar_2019-01-17/tab_delimited/clinvar_2019-01-17_variant_summary.pathogenic.interval_list \ ;