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Picard LiftOverIntervalList needs WARN_ON_MISSING_CONTIG=true

I'm trying to convert a bed file from hg19 to hg38. I'm trying to do this by first converting the bed file to a interval list and lifting it over and then converting it back to bed file. However...

java -jar picard.jar LiftOverIntervalList I=input_hg19.intervals O=output_hg38.intervals SD=/data/homo_sapiens/hg38.dict CHAIN=/data/liftover/hg19ToHg38.over.chain.gz

Stops execution with:

Exception in thread "main" htsjdk.samtools.SAMException: Sequence chr17_KI270860v1_alt from chain file is not found in sequence dictionary.

I'm not interested in the alt contigs, and I've been able to liftover VCF files with (LiftoverVcf) with the argument "WARN_ON_MISSING_CONTIG=true" but it is not available for LiftOverIntervalList. Right now, LiftOverIntervalList is useless for me.

Answers

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