I have 2300 vcf files from 2300 samples generated from haplotypeCaller of GATK from bacteria. Now i want to combine all VCF into one as multivcf sample file. I used CombineVariants from GATK but it is giving error when i give -V *.vcf.gz. I cant write -V file name 2300 times can anybody help me with this?

     java -Xmx8G -jar /home/sark/GenomeAnalysisTK-3.8.1.0/GenomeAnalysisTK.jar -T CombineVariants -R ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta --interval_padding 50  -V *raw.vcf.gz -L ../effluxgenes.bed -o multiple.vcf

Error:

        ##### ERROR
        ##### ERROR MESSAGE: Invalid argument value 'ERR040140_raw.vcf.gz' at position 8.
        ##### ERROR Invalid argument value 'ERR046796_raw.vcf.gz' at position 9.
        ##### ERROR Invalid argument value 'ERR046903_raw.vcf.gz' at position 10.
        ##### ERROR Invalid argument value 'ERR067581_raw.vcf.gz' at position 11.
        ##### ERROR Invalid argument value 'ERR067593_raw.vcf.gz' at position 12.
        ##### ERROR Invalid argument value 'ERR067606_raw.vcf.gz' at position 13.
        ##### ERROR Invalid argument value 'ERR067607_raw.vcf.gz' at position 14.
        ##### ERROR Invalid argument value 'ERR067608_raw.vcf.gz' at position 15.
        ##### ERROR Invalid argument value 'ERR067609_raw.vcf.gz' at position 16.
       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
        ##### ERROR Invalid argument value 'SRR671854_raw.vcf.gz' at position 173.
        ##### ERROR Invalid argument value 'SRR671855_raw.vcf.gz' at position 174.
        ##### ERROR Invalid argument value 'SRR671866_raw.vcf.gz' at position 175.
        ##### ERROR ------------------------------------------------------------------------------------------

Can anyone help me with loop thing?


     (...) -V *raw.vcf.gz (...)

GATK doesnt work like this.

You need

       -V file1.aw.vcf.gz    -V file2.aw.vcf.gz    -V file3.aw.vcf.gz

**or** put all the paths in a file with the   '.list' suffix

$ ls  *raw.vcf.gz > vcf.list

    $ java -Xmx8G -jar  (...) -V vcf.list (...)