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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
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Annotating with CADD #34

Closed landyk01 closed 9 years ago

landyk01 commented 9 years ago

Hello,

I am having trouble with the option to annotate with CADD scores. I downloaded the file containing CADD scores for 1000G SNPs from the CADD website as well as the index file. I am using the latest version of genmod (1.9). Here is my command line:

genmod annotate example/data.vcf -f example/data.ped --cadd_1000g example/1000G.tsv.gz -o example/data.annotated.cadd.vcf

When I use this command the CADD scores are not added to the INFO section of the variants as they are supposed to be. The header of the VCF lists CADD as one of the variables in the INFO section, but none of the variants have the CADD score.

I also tried annotated with a CADD file that contains scores for particular variants that I know are in the VCF with the following command:

genmod annotate example/data.vcf -f example/data.ped --cadd_file example/cadd.tsv -o example/data.annotated.cadd.vcf

This does not add the CADD scores to the INFO section for the variants either.

Any help with this issue would be greatly appreciated!

moonso commented 9 years ago

Hello,

for the second example it could be that the cadd file is not compressed with bgzip (and maybe does not have an index file), I guess this since it does not end with .gz. I will try to replicate the analysis you describe first and see what i get.

moonso commented 9 years ago

Ok so I've tried the latest version just now with the cadd 1000G file and it works perfect. My command: genmod annotate example.vcf -f trio.ped --cadd_1000g 1000G_CADD.tsv.gz -o res.vcf

Not sure what could be the problem for you... Can you try to run with the flag -v/--verbose and post the output?

moonso commented 9 years ago

If it is not sensitive data in your example/data.vcf and example/data.ped you can send them to me via dropbox or something and i can try to run it and see what happens.

moonso commented 9 years ago

I've changed in the example files that are distributed with genmod. You can run them and verify that it works. Good luck!