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Wrong sample order in HaplotypeCaller from contamination file

GERGER Member
edited November 2019 in Ask the GATK team

Hi,
When providing the following file for -contamination-file to HaplotypeCaller:
1401_exome 0.0046493333
1402_exome 0.0012202667
1403_exome 0.0077394667

It outputs this:
06:13:36.154 INFO HaplotypeCallerEngine - The following samples were found in the Contamination file and will be processed at the contamination level therein: [1402_exome, 1401_exome, 1403_exome]

Notice that the order it is listing is different than the order in the contamination file.
So this makes it unclear if HaplotypeCaller is processing the file correctly. I think it is because in the underlying code it is using key values and the output order in this line corresponds to the underlying hashes of the keys. Probably not critical, but just wanted to inform you in case there is an issue in the file processing.

logger.info(String.format("The following samples were found in the Contamination file and will be processed at the contamination level therein: %s", sampleContamination.keySet().toString()));

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