search

pcingola / SnpEff

Other
243 stars 78 forks source link

snpEff annotated vcf file shows no ANN field post analysis #249

Closed rtyb91 closed 4 years ago

rtyb91 commented 4 years ago

I am annotating a list of variants from the canine whole genome sequencings post filtering to retrieve significant candidate genes via SnpEff against the CanFam3.1.99 database.

I ran the command java -Xmx12g -jar snpEff.jar CanFam3.1.99 homo.vcf > homo.ann.vcf

I am currently using SnpEff 5.0

I will attach my vcf file as a reference Homo.vcf.zip

The analysis actually produced a vcd file as well as the results of SnpEff with the genes and their effects, but without the chromosome number attached with them. It would be impossible for us to find out which variant to send for Sanger sequencing without the chromosome number intact. On top of that the annotated vcd did not have an ANN field either. snpEff_genes.txt

Is there something I missed in my command which resulted in the absence of the ANN field?

Many thanks.

pcingola commented 4 years ago

The detailed results for each variant are in the VCF file. The genes.txt is just a summary, as such not suitable for what I understand you want to do. Please use the output VCF file instead.

If the output VCF doesn't have an ANN subfield in the VCS's INFO column, please attach both the input and output files so I can look at them in more detail (no need to attach the whole file, you can just send a few lines of each).