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IntervalListTools UNION incorrectly merges records #1272

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bhanugandham opened this issue Jan 23, 2019 · 1 comment

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@bhanugandham
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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

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 \
;

User question for reference: https://gatkforums.broadinstitute.org/gatk/discussion/comment/55783#Comment_55783

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

@yfarjoun

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commented Apr 16, 2019

should be fixed now. can you check @bhanugandham ?

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