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GATK4 GenotypeGVCFs does not support caret symbol (^) in filenames

buddejbuddej St. LouisMember

The title says it all. When I attempt to run GATK4 (v4.0.3.0) GenotypeGVCFs with the input file A^B^C.g.vcf.gz the following error is produced (full output in attached gatk4-ggvcfs.txt):

[[email protected]] $ /usr/local/genome/gatk-4.0.3.0/gatk GenotypeGVCFs \
  -R ${REFMEM} \
  -V A^B^C.g.vcf.gz \
  -O foo.vcf
...
14:57:22.252 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/user/A%5EB%5EC.g.vcf.gz
...
java.lang.IllegalArgumentException: Illegal character in path at index 1: A^B^C.g.vcf.gz
...
Caused by: java.net.URISyntaxException: Illegal character in path at index 1: A^B^C.g.vcf.gz

Looks like those ^ are getting changed to %5E, which is somehow not interpreted correctly at some point.

This works just fine with GATK 3.x, and interestingly, works just fine when running the following command (full output in attached gatk4-hc.txt):

[[email protected]] $ /usr/local/genome/gatk-4.0.3.0/gatk HaplotypeCaller \
  -R ${REFMEM} \
  -I A^B^C.bam \
  -O foo.g.vcf.gz \
  -ERC GVCF

Sorry in advance for begin a repeat troublemaker

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