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