Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

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

becomes

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

becomes

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 \
;

Answers

Sign In or Register to comment.