I need to overlap two VCF files to find the different mutated loci, variants and detect if there are differences in zygosity between the samples. If anyone knows what I did wrong regarding the input on bcftools or has any suggestions on other tools I can use to perform this type of analysis, the help would be very much appreciated. Thank you in advance and I apologize for the basic question, I am a medical student still learning how to use Galaxy for research.
Hi @Anna
the message points to conflicting settings. It seems you’ve changed Complement to Yes and added something into Nfiles box, resulting in the job error.
For de novo mutations try Complement set to Yes. However, you need to put the “mutant” sample first, and I am not sure how this can be done with the tool. You might consider VCF-VCFintersect.
For changes in zygosity, such as heterozygosity in parental sample and homozygosity in the offspring sample consider using multi-sample VCF and filter it.
Hope this helps.
Kind regards,
Igor
Thank you very much, Igor! As you said, only changing Complement to Yes yielded a result, however, it is not in standard VCF format, the output only contains the colums 1-5 so I can´t annotate it using another software.
Kind regards,
Anna
