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

Hello,

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...)?

Using

java -jar GenomeAnalysisTK.jar \
-T CombineGVCFs \
-R /home/mruhsam/bluebells/Ref_files/refseq_gene236.fa \
--variant *.scc30_sec20.g.vcf \
-o cohort.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?

Thank you

Markus

Best Answer

Answers

  • mruhsammruhsam Member

    Thanks very much!

  • RosmaninhoRosmaninho Member

    @lindenb said:

    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...)?

    find DIR -name "*.g.vcf" > input.list
    

    and then

    java -jar GenomeAnalysisTK.jar -T CombineGVCFs (...) --variant  input.list (...)
    
    

    Does this also work for GenomicsDBImport?

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Yes but you need to use file name extension .txt instead of .list. Somehow the walker gets confused with the file name extension. The parameter to use is -sn and the list must be a tab seperated samplename filename list.

Sign In or Register to comment.