Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

IntervalListTools UNION incorrectly merges records #1272

bhanugandham opened this issue Jan 23, 2019 · 1 comment


Copy link

commented Jan 23, 2019

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 \

User question for reference:

@bhanugandham bhanugandham changed the title `IntervalListTools UNION` incorrectly merges records IntervalListTools UNION incorrectly merges records Jan 23, 2019


This comment has been minimized.

Copy link

commented Apr 16, 2019

should be fixed now. can you check @bhanugandham ?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
None yet
2 participants
You can’t perform that action at this time.