I tried this in the UI using the "Enable batch" setting but it only runs on one VCF and then stops. Any suggestions as to how to get it to run on all input VCF files?
I was able to run a batch job via the GUI. I didn't realize everything that was necessary for running a batch job correctly on the GUI so it took some trial and error to get it working. Thanks!
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One of the suggestions would be to use Swiss Army Knife(link requires log in to RAP) with vcftools, e.g.
vcftools --gzvcf "$in_name" --positions "/mnt/project/example_list_of_positions.txt" --recode --out "$in_prefix".filtered
You can select multiple input VCFs. Then you can merge VCFs using vcf-concat utility.
I tried this in the UI using the "Enable batch" setting but it only runs on one VCF and then stops. Any suggestions as to how to get it to run on all input VCF files?
Can you please try to reproduce batch job using instructions for GUI or CLI?
@Megan Ramaker? were you able to solve this issue? This might benefit to the whole community.
I was able to run a batch job via the GUI. I didn't realize everything that was necessary for running a batch job correctly on the GUI so it took some trial and error to get it working. Thanks!
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