Understanding Indels with no Additional Info in VCF Output

usegalaxy.org support
1

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

2

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:

There was an earlier project to upgrade the GATK tool suite, but it looks like it has been delayed now (see GATK update to 3.4 · Issue #194 · galaxyproject/tools-iuc · GitHub & GATK update to 3.4 · Issue #194 · galaxyproject/tools-iuc · GitHub). 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