BedToIntervalList and IntervalListTools: can interval lists without unique names for intervals be used?Answered
Dear GATK Team,
I have converted multiple BED files for a custom panel to Picard-style interval lists with BedToIntervalList (Picard) prior to merging them to form one interval list with IntervalListTools (Picard). In the documentation for BedToIntervalList, it states:
-Interval name - (Each interval should have a unique name)
whereas IntervalListTools states:
Interval name (ideally unique names for intervals)
However, I have intervals in my lists with the same interval name. Is it still possible to use these interval lists? From my understanding, other types of interval lists do not even have a field for interval name but considering the statements above, could same interval names lead to issues in analysis if not unique?
Thank you for your time and help.
I am going to move your post into our Community Discussions -> Documentation Questions topic, as the "Other" topic is for reporting bugs and issues with GATK.
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ISmolicz With what GATK tools will you be using the interval list?
Thank you for your reply Genevieve Brandt.
At present, I am using an interval list with the following GATK tools: GenomicsDBImport, Mutect2, GetPileupSummaries and DepthOfCoverage.
In addition, I use an interval list with the following Picard tools: CollectSequencingArtifactMetrics, CollectHsMetrics (two separate lists) and CollectVariantCallingMetrics.
Have there been any warning messages or issues with those tools and the interval list without unique names?
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