I've produced a set of about 400 of GVCF files with gatk HaplotypeCaller, with the `-ERC GVCF` option. I'd now like to combine them for downstream genotyping and variant recalibration. I believe I can combine with gatk CombineGVCFs.

    gatk CombineGVCFs \
       -R reference.fasta \
       --variant sample1.g.vcf.gz \
       --variant sample2.g.vcf.gz \
       -O cohort.g.vcf.gz


But what I don't know, is how to input all my 400 GVCF files into CombineGVCFs. I've heard this can be done with the `--arguments_file` option, but I don't know how to build such a file?

Any help gratefully received!

create a file with the `.list` suffix containing the path to your vcf

    find /path/to/dir -type f -name "*.vcf.gz" > input.list

and then use this file with the '-V' argument

    (...)    --variant input.list

