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CombineGVCFs tool issues

Dear Gatk team,

I am using CombineGVCFs tool to join vcf file to one vcf file, I have more that 1000 vcf files and its very noisy to list them in the CombineGVCFs command so I made them in gVCF_list.txt, and for testing purpose I just used 2 vcf files:

/Sakhaa/GVCF/S_18_2123_NIST-8398_AD008_L008.snps.indels.g.vcf.gz
/Sakhaa/GVCF/M_18_3111_H-7_D707-D506_L007.snps.indels.g.vcf.gz

and read the list as the following

gVCF_list=$GVCF/gVCF_list.txt
GVCF_list=$(while read line; do echo '-V' $line; done < "$gVCF_list")

output:

-V /Sakhaa/GVCF/S_18_2123_NIST-8398_AD008_L008.snps.indels.g.vcf.gz  -V /Sakhaa/GVCF/M_18_3111_H-7_D707-D506_L007.snps.indels.g.vcf.gz

The CombineGVCFs looks like this:

gatk CombineGVCFs echo ${GVCF_list} -R $REF --output $VCF/combinedgvcf.Mix.vcf.gz

and I got this error:


*********************************************************************** A USER ERROR has occurred: Argument output was missing: Argument 'output' is required. ***********************************************************************

The output is written in the code, may I ask anyone to help me for solving that issue in the command?

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @Sakhaa , Interesting. It looks like you didn't pass the gvcf list using --variant or -V. You should be able to provide a .list text file listing the set of gVCFs to be combined, one file per line. If you are still getting issues please post your error log. Thanks!

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