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wwylab / MuSE

Somatic point mutation caller
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Error: The index of dbSnp.vcf.gz either does not exist or is older than the vcf file. #12

Closed AnnaMontaner closed 12 months ago

AnnaMontaner commented 1 year ago

Hi,

I'm trying to run MuSE on a set of paired tumour and normal samples and I'm running into this error after the sump command. I have my gzipped dbSnp database and its .tbi in the same folder and they were created the same day, so I really don't know what is going on. I have also noted that my reference genome is GRCh38.p13 while the one used in dbSnp is GRCh38.p7. However, this hasn't given any problems when using dbSnp in the context of variant annotation with SnpEff for instance, so I'm not sure this could be a possible explanation.

Any advice on how to solve this issue ?

Thanks

Anna

wwylab commented 1 year ago

what is the error message Anna?

jiyunmaths commented 12 months ago

Hi @AnnaMontaner, can you run 'tabix -p vcf your_dbSnp.vcf.gz' and run MuSE sump again? If you the error still happens, please share the error message with us. Thanks.

AnnaMontaner commented 12 months ago

Sorry @wwylab I wrote the error in the issue title but not in my message... The error is "The index of dbSnp.vcf.gz either does not exist or is older than the vcf file."

Thanks for your suggestion @jiyunmaths

Anna

wwylab commented 12 months ago

issue resolved.

AnnaMontaner commented 12 months ago

It worked, thanks!