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Multiple GVCF inputs for GenotypeGVCFs
I tried to use GenotypeGVCFs to perform joint genotyping with 5 samples. I used -V mygvcfs.list to submit multiple gvcfs, but I got the following error message:
Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types.
So, I run again with -V:VCF mygvcfs.list. I got another error:
Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file
I checked back my gvcfs, the #CHROM header line is present. I also tried to run GeotypeGVCFs by typing the input gvcfs one by one on command line, and it works well.
Any suggestion on why this happened and how can I submit the input gvcfs in list?
I am using GATK version: 3.3.0