Dear bioconductor team, I have a problem with predictCoding() of the VariantAnnotation library posing an error which is the same as described here: https://stat.ethz.ch/pipermail/bioconductor/2012-November/048940.html Howerver, after reading my vcf it clearly has a DNAStringSetList in it's ALT variable. The problem remains when using vcftools to remove indels from the vcf. As far as I see there are some ALTs with two possibilities. Is there anything else which could cause the problem? I am also aware of this thread https://stat.ethz.ch/pipermail/bioconductor/2012-October/048370.html but I can't figure out how to remove those lines causing the problem. Thank you very much J?rg vcf=readVcf("file.vcf","hg") coding <- predictCoding(vcf, txdb, seqSource=fa) Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup, skipcode, : in 'x[[6655]]': not a base at pos 3 > alt(vcf) DNAStringSetList of length 142721 [[1]] C [[2]] T [[3]] G [[4]] G [[5]] G [[6]] C [[7]] C [[8]] A [[9]] G [[10]] C .. <142711 more elements> > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

Hi J?rg, It looks like your sessionInfo() output was cut off and I can't tell what version of VariantAnnotation you have. Versions >= 1.10.0 detect structrural variants and create either a CharacterList or DNAStringSetList. Since you have a DNAStringSetList, all values should be valid bases. Does this return TRUE? hasOnlyBaseLetters(unlist(alt(vcf))) Are there any non-base characters in the matrix? alphabetFrequency(unlist(alt(vcf))) To help further I'll need the version of VariantAnnotation and a reproducible example. Valerie On 06/17/2014 05:45 AM, "Dr. J?rg Linde" wrote: > Dear bioconductor team, > > I have a problem with predictCoding() of the VariantAnnotation library > posing an error which is the same as described here: > https://stat.ethz.ch/pipermail/bioconductor/2012-November/048940.html > > Howerver, after reading my vcf it clearly has a DNAStringSetList in > it's ALT variable. > The problem remains when using vcftools to remove indels from the vcf. > As far as I see there are some ALTs with two possibilities. > Is there anything else which could cause the problem? > > I am also aware of this thread > https://stat.ethz.ch/pipermail/bioconductor/2012-October/048370.html > but I can't figure out how to remove those lines causing the problem. > > Thank you very much > J?rg > > vcf=readVcf("file.vcf","hg") > coding <- predictCoding(vcf, txdb, seqSource=fa) > Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup, > skipcode, : > in 'x[[6655]]': not a base at pos 3 > > alt(vcf) > DNAStringSetList of length 142721 > [[1]] C > [[2]] T > [[3]] G > [[4]] G > [[5]] G > [[6]] C > [[7]] C > [[8]] A > [[9]] G > [[10]] C > .. > <142711 more elements> > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Valerie Obenchain Program in Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, Seattle, WA 98109 Email: vobencha at fhcrc.org Phone: (206) 667-3158

Hi, Please remember to hit 'reply all' when responding so we keep communication on the list. If you're interested in mapping the ambiguity codes in alt to their base-pair equivalents see ?IUPAC_CODE_MAP in the Biostrings package. To identify rows with ambiguous codes you can use the 'other' column output from alphabetFrequency(): alt <- DNAStringSetList("WA", "G", "NA", c("AG", "M"), "A") af <- alphabetFrequency(unlist(alt), baseOnly=TRUE) ambiguous <- any(relist(af[,"other"] > 0L, alt)) > ambiguous [1] TRUE FALSE TRUE TRUE FALSE A VCF can be subset by rows (variants) or columns (samples) using '['. Remove ambiguous rows and keep all samples: vcf[!ambiguous, ] Valerie On 06/19/2014 03:28 AM, "Dr. J?rg Linde" wrote: > Dear Valerie, > thank you sooo much. Helped a lot. Version is VariantAnnotation_1.8.13. > > >hasOnlyBaseLetters(unlist(alt(vcf))) > FALSE > > > > unlist(alt(vcf))[rowSums(alphabetFrequency(unlist(alt(vcf)))[,5:1 7])>0] > A DNAStringSet instance of length 11 > width seq > [1] 2 GN > [2] 2 WA > [3] 12 GTATGTGTNTAT > [4] 2 NA > [5] 2 YC > ... ... ... > [7] 6 AGANGA > [8] 2 GN > [9] 6 MCAATA > [10] 11 GTAGTANTAGT > [11] 2 TN > > > I am just looking for an elegant way to remove these lines from my vcf > > best > J?rg > > > > > On 06/18/2014 10:17 PM, Valerie Obenchain wrote: >> Hi J?rg, >> >> It looks like your sessionInfo() output was cut off and I can't tell >> what version of VariantAnnotation you have. >> >> Versions >= 1.10.0 detect structrural variants and create either a >> CharacterList or DNAStringSetList. Since you have a DNAStringSetList, >> all values should be valid bases. >> >> Does this return TRUE? >> >> hasOnlyBaseLetters(unlist(alt(vcf))) >> >> Are there any non-base characters in the matrix? >> >> alphabetFrequency(unlist(alt(vcf))) >> >> >> To help further I'll need the version of VariantAnnotation and a >> reproducible example. >> >> Valerie >> >> >> >> On 06/17/2014 05:45 AM, "Dr. J?rg Linde" wrote: >>> Dear bioconductor team, >>> >>> I have a problem with predictCoding() of the VariantAnnotation library >>> posing an error which is the same as described here: >>> https://stat.ethz.ch/pipermail/bioconductor/2012-November/048940.html >>> >>> Howerver, after reading my vcf it clearly has a DNAStringSetList in >>> it's ALT variable. >>> The problem remains when using vcftools to remove indels from the vcf. >>> As far as I see there are some ALTs with two possibilities. >>> Is there anything else which could cause the problem? >>> >>> I am also aware of this thread >>> https://stat.ethz.ch/pipermail/bioconductor/2012-October/048370.html >>> but I can't figure out how to remove those lines causing the problem. >>> >>> Thank you very much >>> J?rg >>> >>> vcf=readVcf("file.vcf","hg") >>> coding <- predictCoding(vcf, txdb, seqSource=fa) >>> Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup, >>> skipcode, : >>> in 'x[[6655]]': not a base at pos 3 >>> > alt(vcf) >>> DNAStringSetList of length 142721 >>> [[1]] C >>> [[2]] T >>> [[3]] G >>> [[4]] G >>> [[5]] G >>> [[6]] C >>> [[7]] C >>> [[8]] A >>> [[9]] G >>> [[10]] C >>> .. >>> <142711 more elements> >>> > sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >