This applet performs the merging of VCFs through bcftools. If working with WGS VCFs, you should consider trimming down data that may not be required for subsequent analysis of the merged VCFs. Here is an applet that performs such operations.
Clone this github repo to a local directory:
git clone https://github.com/drarwood/vcf_merger
Navigate to a relevant directory within the project directory on the DNAnexus platform to install the applet
dx cd /path/to/install/apps
Now you are ready to build and upload the applet to the DNAnexus plaform directory:
dx build -f vcf_merger
Navigate to the RAP directory where you want the output to be directed:
dx cd /path/to/where/the/output/should/go
Simply run the applet by specifying the name (and path if required) of the *.vcf.gz input VCF and the filename of the output GDS.
Note priority is set to high below which is recommended for long processes to avoid jobs potentially being reset when running as normal priority jobs (see dx run on changing job priority):
dx run /path/to/install/apps/vcf_merger \
-ivcf_file_list=/path/to/vcf/file/list.txt \
-imerged_vcf_filename=my_data_merged.vcf.gz \
--priority high \
-y