Question: SNPEff, SNPSift errors
0
gravatar for agata88
4.6 years ago by
agata88800
Poland
agata88800 wrote:

Hi,

I am trying to use SNPEff and SNPSift since yesterday and it really makes me crazy. I am not even able to get through tutorial. For example:

"Annotate ID field using dbSnp Note: SnpSift will automatically download and uncompress dbSnp database if not locally available. java -jar SnpSift.jar annotate -dbsnp file.vcf > file.dbSnp.vcf"

No it's not automatically download!

Error below (even on their example file):

Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: File not found '/home/kot/Pulpit/databases/snpEff/./db/GRCh38/dbSnp/dbSnp.vcf.gz'

My first question is, why this program is looking for GRCh38 while I am using CRCH37, and how can I make through this???

Could anybody write a command line for this programs to get the annotation for vcf file from dbsnp, clinvar, 1000genomes etc?

I would really appreciate for any help.

Best,

Agata

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