Understanding Indels with no Additional Info in VCF Output

[Debanjan_Roy]

Dear all,
Using GATK pipeline, I am getting indels with no additional information in the other columns in the VCF file. One thing is that if there is no information available for a variant, the column is filled with a dash( and the additional columns are not just blank). But the indels which I am talking about have just blank columns for the additional info fields.

        So, my question is whether those indels are some false positives reported by GATK or there can be variants with such blank columns in the VCF output?

Thanks in advance
Debanjan Roy

[jennaj]

Yes, this is a possible result. Please see this post for how to interpret vcf output from the GATK pipeline: https://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it

That said, all GATK tools currently wrapped for Galaxy have been deprecated. Problems can come up (functional and technical) and the tools should be avoided.

Please see the GTN Variant Analysis tutorials for help with using alternative tools/methods:

Troubleshooting resources for errors or unexpected results

Galaxy Training Network Tutorials : Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

There was an earlier project to upgrade the GATK tool suite, but it looks like it has been delayed now (see https://github.com/galaxyproject/tools-iuc/issues/194 & https://github.com/galaxyproject/tools-iuc/issues/194). I asked the IUC about future plans/status at their Gitter chat – please watch for their reply here and/or free to join in: https://gitter.im/galaxy-iuc/iuc?at=5c7d5c6153efa91203b107ca