Dear Vincent, You're right! The vcf was actually successfully read and created. So, problem solved, a user error. Older version of the package seems to give an error, though, and since I was running these in parallel, I mixed the two sessions. Sorry about that. - Jarno On Mon, Nov 12, 2012 at 1:12 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > what you reported is a warning, not an error. did the object "vcf" get > created? > > On Mon, Nov 12, 2012 at 4:39 AM, Jarno Tuimala <jtuimala at="" gmail.com=""> wrote: >> >> Hello! >> >> I have a problem reading a VCF file with the VariantAnnotation >> package. The filtered VCF file (attached as text below) has been >> generated with vcftools. >> >> This is what I tried in R and the resulting error message: >> >> > library(VariantAnnotation) >> > vcf<-readVcf("vcftools.filtered.vcf", "hg19") >> >> Warning message: >> In doTryCatch(return(expr), name, parentenv, handler) : >> record 1 (and others?) INFO '.' not found >> >> If I understood it correctely, the dots in the INFO column of the VCF >> file create the problem. >> >> Is there an alternative way to read this vcf file and annotate it with >> VariantAnnotation package? >> >> Best Regards, >> Jarno >> >> >> ---- >> >> This is the session info: >> >> R version 2.15.1 Patched (2012-07-25 r59963) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=Finnish_Finland.1252 LC_CTYPE=Finnish_Finland.1252 >> LC_MONETARY=Finnish_Finland.1252 LC_NUMERIC=C >> LC_TIME=Finnish_Finland.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] VariantAnnotation_1.4.3 Rsamtools_1.10.1 Biostrings_2.26.2 >> GenomicRanges_1.10.2 IRanges_1.16.3 >> BiocGenerics_0.4.0 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.20.2 Biobase_2.18.0 biomaRt_2.14.0 >> bitops_1.0-4.1 BSgenome_1.26.1 DBI_0.2-5 >> GenomicFeatures_1.10.0 parallel_2.15.1 >> [9] RCurl_1.95-1.1 RSQLite_0.11.2 rtracklayer_1.18.0 >> stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 >> zlibbioc_1.4.0 >> >> >> And this is the VCF file: >> >> ##fileformat=VCFv4.1 >> ##samtoolsVersion=0.1.18 (r982:295) >> ##INFO=<id=dp,number=1,type=integer,description="raw read="" depth"=""> >> ##INFO=<id=dp4,number=4,type=integer,description="# high-quality="">> ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> >> ##INFO=<id=mq,number=1,type=integer,description="root-mean-square>> mapping quality of covering reads"> >> ##INFO=<id=fq,number=1,type=float,description="phred probability="" of="">> all samples being the same"> >> ##INFO=<id=af1,number=1,type=float,description="max-likelihood>> estimate of the first ALT allele frequency (assuming HWE)"> >> ##INFO=<id=ac1,number=1,type=float,description="max-likelihood>> estimate of the first ALT allele count (no HWE assumption)"> >> ##INFO=<id=g3,number=3,type=float,description="ml estimate="" of="" genotype="">> frequencies"> >> ##INFO=<id=hwe,number=1,type=float,description="chi^2 based="" hwe="" test="">> P-value based on G3"> >> ##INFO=<id=clr,number=1,type=integer,description="log ratio="" of="">> genotype likelihoods with and without the constraint"> >> ##INFO=<id=ugt,number=1,type=string,description="the most="" probable="">> unconstrained genotype configuration in the trio"> >> ##INFO=<id=cgt,number=1,type=string,description="the most="" probable="">> constrained genotype configuration in the trio"> >> ##INFO=<id=pv4,number=4,type=float,description="p-values for="" strand="">> bias, baseQ bias, mapQ bias and tail distance bias"> >> ##INFO=<id=indel,number=0,type=flag,description="indicates that="" the="">> variant is an INDEL."> >> ##INFO=<id=pc2,number=2,type=integer,description="phred probability="" of="">> the nonRef allele frequency in group1 samples being larger (,smaller) >> than in group2."> >> ##INFO=<id=pchi2,number=1,type=float,description="posterior weighted="">> chi^2 P-value for testing the association between group1 and group2 >> samples."> >> ##INFO=<id=qchi2,number=1,type=integer,description="phred scaled="" pchi2."=""> >> ##INFO=<id=pr,number=1,type=integer,description="# permutations="">> yielding a smaller PCHI2."> >> ##INFO=<id=vdb,number=1,type=float,description="variant distance="" bias"=""> >> ##FORMAT=<id=gt,number=1,type=string,description="genotype"> >> ##FORMAT=<id=gq,number=1,type=integer,description="genotype quality"=""> >> ##FORMAT=<id=gl,number=3,type=float,description="likelihoods for="">> RR,RA,AA genotypes (R=ref,A=alt)"> >> ##FORMAT=<id=dp,number=1,type=integer,description="# high-quality="" bases"=""> >> ##FORMAT=<id=sp,number=1,type=integer,description="phred-scaled strand="">> bias P-value"> >> ##FORMAT=<id=pl,number=g,type=integer,description="list of="">> Phred-scaled genotype likelihoods"> >> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT >> HG00171 HG00174 NA18486 NA18489 >> 20 6731335 . T C 80.5 . . GT:PL:GQ >> 1/1:0,0,0:3 1/1:0,0,0:3 1/1:0,0,0:3 1/1:113,12,0:13 >> 20 6732603 . A T 25.7 . . GT:PL:GQ >> 0/0:0,6,54:8 0/0:0,0,0:3 0/0:0,0,0:3 0/1:58,0,27:35 >> 20 6736189 . A G 47.8 . . GT:PL:GQ >> 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 1/1:79,6,0:6 >> 20 6736562 . C A 20.4 . . GT:PL:GQ >> 0/0:0,0,0:4 0/0:0,0,0:4 0/1:53,0,32:40 0/0:0,9,98:11 >> 20 6737384 . A G 62 . . GT:PL:GQ >> 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:92,0,95:92 >> 20 6737551 . G A 26.3 . . GT:PL:GQ >> 1/1:30,3,0:4 0/1:0,3,40:4 0/1:0,0,0:3 1/1:34,3,0:4 >> 20 6738766 . T A 34.3 . . GT:PL:GQ >> 0/1:0,0,0:3 0/0:0,3,33:4 0/1:0,0,0:3 1/1:69,6,0:4 >> 20 6739398 . G A 64 . . GT:PL:GQ >> 1/1:0,0,0:3 1/1:0,0,0:3 1/1:0,0,0:3 1/1:96,9,0:10 >> 20 6740366 . C T 25.8 . . GT:PL:GQ >> 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 1/1:57,6,0:6 >> 20 6740850 . G A 34.4 . . GT:PL:GQ >> 0/1:0,0,0:3 0/0:0,6,59:6 0/1:0,0,0:3 1/1:70,6,0:3 >> 20 6743016 . T C 87.2 . . GT:PL:GQ >> 0/1:0,0,0:3 0/1:0,3,31:3 0/1:0,0,0:3 1/1:124,12,0:10 >> 20 6743306 . A C 39.8 . . GT:PL:GQ >> 0/1:0,0,0:3 1/1:71,6,0:6 0/1:0,0,0:3 0/1:0,0,0:3 >> 20 6746498 . C T 17.4 . . GT:PL:GQ >> 0/1:0,0,0:3 0/0:0,3,38:4 0/1:31,3,0:4 0/1:24,0,54:26 >> 20 6749158 . C A 18.3 . . GT:PL:GQ >> 0/0:0,3,29:8 0/0:0,3,32:8 0/1:53,0,30:40 0/0:0,21,159:25 >> 20 6749671 . A C 21.3 . . GT:PL:GQ >> 0/0:0,9,65:7 0/1:33,3,0:3 0/1:28,3,0:3 0/1:0,0,0:3 >> 20 6751034 . A G 999 . . GT:PL:GQ >> 0/0:0,24,189:19 0/1:33,0,141:38 1/1:255,105,0:99 1/1:255,66,0:65 >> 20 6751316 . A G 155 . . GT:PL:GQ >> 0/0:0,3,22:4 0/0:0,6,43:6 1/1:116,12,0:8 0/1:84,0,25:29 >> 20 6754246 . G A 16.4 . . GT:PL:GQ >> 0/0:0,0,0:3 0/0:0,3,20:6 0/0:0,0,0:3 0/1:48,0,43:45 >> 20 6755598 . T G 46 . . GT:PL:GQ >> 1/1:0,0,0:3 1/1:0,0,0:3 1/1:0,0,0:3 1/1:78,9,0:10 >> 20 6756217 . G A 14.2 . . GT:PL:GQ >> 0/0:0,3,38:7 0/0:0,3,38:7 0/0:0,0,0:4 0/1:47,0,26:34 >> 20 6760431 . C A 36.8 . . GT:PL:GQ >> 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 1/1:68,6,0:6 >> 20 6761512 . C T 104 . . GT:PL:GQ >> 1/1:0,0,0:3 1/1:0,0,0:3 1/1:0,0,0:3 1/1:136,12,0:13 >> 20 6762025 . G A 29.3 . . GT:PL:GQ >> 0/1:0,3,37:4 1/1:32,3,0:4 0/1:0,0,0:3 1/1:35,3,0:4 >> 20 6765841 . A C 35.3 . . GT:PL:GQ >> 0/0:0,3,31:4 0/1:0,0,0:3 0/1:0,0,0:3 1/1:70,6,0:4 >> 20 6767119 . G C 104 . . GT:PL:GQ >> 1/1:0,0,0:3 1/1:0,0,0:3 1/1:0,0,0:3 1/1:136,12,0:13 >> 20 6767354 . C T 24 . . GT:PL:GQ >> 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:54,0,111:55 >> 20 6767543 . T C 14.2 . . GT:PL:GQ >> 0/0:0,3,31:7 0/0:0,3,32:7 0/0:0,0,0:4 0/1:47,0,22:30 >> 20 6769102 . T TC 117 . . GT:PL:GQ >> 1/1:0,0,0:6 1/1:40,3,0:9 1/1:40,3,0:9 1/1:80,6,0:11 >> 20 6769533 . G A 21.4 . . GT:PL:GQ >> 0/1:0,0,0:3 0/0:0,6,64:6 0/1:0,0,0:3 1/1:57,6,0:3 >> 20 6769676 . A G 27.2 . . GT:PL:GQ >> 0/0:0,3,32:5 0/0:0,3,34:5 0/0:0,0,0:3 0/1:64,6,0:3 >> 20 6769714 . T C 63.2 . . GT:PL:GQ >> 1/1:68,6,0:9 1/1:0,0,0:4 1/1:0,0,0:4 1/1:29,3,0:7 >> 20 6769877 . T C 14.5 . . GT:PL:GQ >> 0/1:27,0,27:27 0/1:0,0,0:3 0/0:0,6,68:6 0/1:26,3,0:4 >> 20 6769893 . C A 16.7 . . GT:PL:GQ >> 0/0:0,3,38:5 0/0:0,0,0:3 0/0:0,6,63:8 0/1:54,6,0:4 >> >> _______________________________________________ >> 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 > >