Dealing with GATK illegal character

Question

[MAPK]

I am trying to run genomicsdbImport in GATK.

/gatk --java-options "-Xms4G -Xmx32G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" GenomicsDBImport \
--genomicsdb-workspace-path ${WORKDIR} \
       --batch-size 50 \
       -L chrX \
       --sample-name-map ${mylist.list} \
       --tmp-dir=${tmpPATH} \
       --max-num-intervals-to-import-in-parallel 10 \
       --reader-threads 16

I am supplying a list of gvcfs in the command above. I have gvcf file names with sample_name^Barcode^project_name (mylist.list). With this input, gatk is giving me illegal character error for input gvcf files because of ^. Is there a way to deal with this without renaming the input gvcf files? This is my mylist.list:

CAP_100       /dir/CAP_100^8036056040^201909_SEY.aln.srt.isec-paddedexome.markd.recal.raw.snps.indels.g.vcf.gz       
CAP_28       /dir/CAP_28^8036056033^201909_SEY.aln.srt.isec-paddedexome.markd.recal.raw.snps.indels.g.vcf.gz       
CAP_2       /dir/CAP_2^8036056474^201909_SEY.aln.srt.isec-paddedexome.markd.recal.raw.snps.indels.g.vcf.gz

This is the error message I am getting:

A USER ERROR has occurred: Malformed URI java.net.URISyntaxException: Illegal character in path at index 49: /dir/CAP_100^8036056040^201909_SEY.aln.srt.isec-paddedexome.markd.recal.raw.snps.indels.g.vcf.gz

[Ram]

You can try escaping the ^ characters, like so:

CAP_100       /dir/CAP_100\^8036056040\^201909_SEY.aln.srt.isec-paddedexome.markd.recal.raw.snps.indels.g.vcf.gz       
CAP_28       /dir/CAP_28\^8036056033\^201909_SEY.aln.srt.isec-paddedexome.markd.recal.raw.snps.indels.g.vcf.gz       
CAP_2       /dir/CAP_2\^8036056474\^201909_SEY.aln.srt.isec-paddedexome.markd.recal.raw.snps.indels.g.vcf.gz

Using a caret in a filename was a bad idea. You're better off either renaming the files or creating softlinks with clean names to these files.

cd /dir/
ln -s CAP_100\^8036056040\^201909_SEY.aln.srt.isec-paddedexome.markd.recal.raw.snps.indels.g.vcf.gz CAP_100__8036056040.softlink.vcf.gz

[MAPK]

Escaping character did not work. I will try with soft links.