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IntervalListTools UNION corner case: doesn't keep all name fields if merged coordinates are same

myourshawmyourshaw University of ColoradoMember ✭✭

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 \
-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 \


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