Error while running gatk CombineGVCFs
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16 months ago
kmkdesilva ▴ 90

Hi everyone,

I am trying to combine 35 gvcf files. I used gatk/4.1.3.0 CombineGVCFs to do this. I used the format given in their website.

 gatk CombineGVCFs \
   -R reference.fasta \
   --variant sample1.g.vcf.gz \
   --variant sample2.g.vcf.gz \
   -O cohort.g.vcf.gz

my command:

gatk  CombineGVCFs   -R /path to reference.fa  -V /path to 1.gvcf.gz  -V /path to 2.gvcf.gz  -V /path to 3.gvcf.gz .........-V /path to 35.gvcf.gz  -O /path to output.gvcf.gz

I tried both --variant and -V I keep getting the error "A USER ERROR has occurred: Invalid argument 'V'. I appreciate your help

gatk CombineGVCF USER ERROR • 779 views
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write the real command, not those -V /path to x.vcf which are already wrong (spaces in filename)

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