Error while adding annotation SnpEff

[Jemkon]

Hello,

I would like to try SMuRF to predict variants from BAM.

Here what I run on test files.

myresults <- smurf(mydir, "combined")

 Completed but with warning:

Time difference of 15.69459 secs
 Warning messages:
 1: In FUN(X[[i]], ...) :
   duplicate ID's in header will be forced to unique rownames
2: In FUN(X[[i]], ...) :
   duplicate ID's in header will be forced to unique rownames

Then I run.....
myresults <- smurf(mydir, "cdsannotation") 

 .....
[1] "Predicting SNVs" 
|======================================================================| 100% 
|======================================================================| 100%

[1] "Predicting INDELs"
|======================================================================| 100% 
|======================================================================| 100%

[1] "SNV annotation"
[1] "Adding CDS and annotations"
[1] "reading mutect2"  
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ?scanVcf? for signature ?"character", "GRanges"?
 In addition: Warning messages:
 1: In FUN(X[[i]], ...) :
   duplicate ID's in header will be forced to unique rownames
 2: In FUN(X[[i]], ...) :
   duplicate ID's in header will be forced to unique rownames

I would really like to get variants with annotations from SnpEff/SnpSift. How do i get it from SMuRF. Do I have to run SMuRF first and then save the output to vcf, which then parsed to SnpEff?

Many thanks.

[tyler5huang]

Hi Jemkon, apologies, please have your .vcf files tabix indexed as the annotations require an indexed .tbi file. For example tabix –p vcf *.vcf.gz on the unix console, for the mutect2, vardict, varscan and freebayes vcf files. Thanks