Hi @jennaj,
thanks for your response.
I used the tool “SnpEff download” to download the SnpEff annotation database. The following is an extract from the stderr with further information regarding the version.
“|00:00:00|SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani|
|—|---|
|00:00:00|Command: ‘download’|
|00:00:00|Reading configuration file ‘snpEff.config’. Genome: ‘GRCh37.75’|
|00:00:00|Reading config file: /data/dnb02/galaxy_db/job_working_directory/006/494/6494647/working/snpEff.config|
|00:00:00|Reading config file: /usr/local/tools/_conda/envs/__snpeff@4.3.1t/share/snpeff-4.3.1t-0/snpEff.config|
|00:00:03|done|
|00:00:03|Downloading database for ‘GRCh37.75’|
|00:00:05|Connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_GRCh37.75.zip|
|00:00:06|Following redirect: https://netcologne.dl.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_GRCh37.75.zip|
|00:00:07|Local file name: ‘/tmp/snpEff_v4_3_GRCh37.75.zip’|”
To my understanding SnpEff version 4.3 is the newest available on https://sourceforge.net/projects/snpeff/files/databases/ .
So I am still confused, why I have a slight difference in the annotated information for one of my example variants compared to the output of the variant effect predictor. (Missing information ( WARNING_TRANSCRIPT_NO_START_CODON) for ENST00000595514). Do you have another idea?
I think my second question was misleading. When checking the annotated information with VEP (Variant Effect Predictor by Ensemble) I had to find out that VEP does not supply the HGVSc for upstream and downstream variants. So I was wondering if there is another option to check the HGVSc for upstream and downstream variants? Or if I am going to far and don’t have to do this as I can be sure that using the tool snpeff eff annotate with the downloaded snpeff database on usegalaxy.eu without an error, that the annotation worked fine?
Thanks for the information regarding the QC and renaming chromosome. As I ran the bcftools norm after variant calling and before annotation, I thought this would be sufficient to make sure the vcf is compatible for annotation afterwards (as recommended in the “somatic variant tutorial”). Am I wrong?
Thanks a lot for your help!
All the best,
Rose