We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
CombineGVCFs input multiple files
How can I specify the multiple input files for CombineGVCF without having to type the name of each file separately (I have 432 input files...)?
java -jar GenomeAnalysisTK.jar \
-T CombineGVCFs \
-R /home/mruhsam/bluebells/Ref_files/refseq_gene236.fa \
--variant *.scc30_sec20.g.vcf \
gives me the error message
ERROR MESSAGE: Invalid argument value '12663.gatkHC.raw.snps.indels_scc30_sec20.g.vcf ' at position 6.
ERROR Invalid argument value '187-03.gatkHC.raw.snps.indels_scc30_sec20.g.vcf ' at position 7.
ERROR Invalid argument value '188-02.gatkHC.raw.snps.indels_scc30_sec20.g.vcf ' at position 8.
ERROR Invalid argument value '232-01.gatkHC.raw.snps.indels_scc30_sec20.g.vcf ' at position 9.
AND SO ON going through all the 432 sample names. However, specifying a few files separately using '–variant' works. Surely there must be a way to 'batch' specify the name of the input files?