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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 \ ;