Hi!
I have two different types of VCF files. The first, complete:
and the second:
(only the first locus is shown)
Both files have the following properties:
Tried VCFcombine to combine them with no success...
How can I combine them?
Should I first finish processing the second file? (how?)
Thank you in advance for the help!
Luca
Hello,
If the job creating the second VFC file was not complete when you wrote in, try the tool now.
The tool will only work on two VFC files in strict format, with the "vcf" datatype assigned, and based on the same exact reference dataset (genome/transcriptome/exome).
I am not exactly clear what you mean by two different types of VCF files so am assuming that this refers to the state of the job (running versus queued). I am also unclear about how the tool fails (fails to find inputs, fails to launch, fails with an error) - so please clarify this is you need more feedback.
Best, Jen, Galaxy team
Hi Jen,
I think I was not clear enough...my bad!
With "two different types" I mean I have some files which seem to be at different levels of analysis.
The first seem to be filtered and has the ALT SNVs indicated, while the second has many more SNVs with no ALT.
Indeed when I try VCF combine on two files of the first type, the merge works.
Conversely, when I try to combine two files of the second type the process runs completely but the SNVs are not combined.
Thank you for your support!
Luca
The annotation has to be a match for this tool to combine it. This is with respect to content, but that distills down to format, programmatically, when making calculating the "match" for a merge. Tools to add in, remove, or otherwise modify annotation are in the groups VCF Manipulation and Variant Analysis.
That's what I thought...can I ask you how you would proceed or should I make a brand new question?
Thank you!
I can reply .. annotating both to have the same level/type/format of annotation is the goal. Adding it in may be possible, but seems like that might lead to some fussing to get it all consistent. Instead, I would probably strip this content from both files and add in the annotation all over again to both, using the same exact tools, to ensure consistency - then merge.
The problem is that I don't know which tools and, most importantly, which datasets have been used... Tried VCF-BEDintersect+VCFaddinfo to filter and annotate before using VCFcombine. The two files are combined as usual: extra sample columns are added on the right but the single raws just cannot be merged :(
