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FunGeST / Palimpsest

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
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Error in getting DSB #45

Closed beginner984 closed 4 years ago

beginner984 commented 4 years ago

Hello

I have used vcd_annotate function successfully but for DSB I get this error

DBS_input <- palimpsest_input(vcf = vcf, Type = "DBS")
Error in if (res$DBS_cat[i] == res$DBS_cat[i - 1] & res$Sample[i] == res$Sample[i -  : 
  missing value where TRUE/FALSE needed

I could not find the reason in google search Please you may help?

Thanks

benedict909 commented 4 years ago

Hello,

Thanks for getting in touch and sorry for not getting back to you sooner.

This error is likely caused by Palimpsest not being able to find any DBS mutations in your vcf. I would suggest you check that the VCF has been correctly ordered by Sample>CHROM>POS, as palimpsest_input needs these to be in the right order for DBS mutations to be counted.

If you are still having this problem I would be happy to take a look at some of your example data.

Best wishes, Benedict