readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
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Entering edit mode
jls2282 • 0
@jls2282-7127
Last seen 5.4 years ago
United States

 

I am having a problem reading the info field on vcf files generated by

the NextGene software. Here is an example:

vcfF is the vcf report as exported from NextGene

>hdr=scanVcfHeader(vcfF)
> rownames(info(hdr))
 [1] "NS"                                            "DP"                                            "AF"                                            "SGACOV"                                       
 [5] "SGASCORE"                                      "SGGENEDIR"                                     "SGANNOT"                                       "SGREFAA"                                      
 [9] "SGAAC"                                         "SGMRNAID"                                      "SGCDSID"                                       "SGTI"                                         
[13] "SGPI"                                          "SGGI"                                          "SGSEGDES"                                      "SGSEGPOS"                                     
[17] "SGAMBGAINPEN"                                  "SGAMBLOSSPEN"                                  "SG_Cosmic(Cosmic_68)_68_COSMIC_ID"             "SG_Cosmic(Cosmic_68)_68_COSMIC_Count"         
[21] "SG_dbNSFP(dbNSFP_2.0)_2_SIFT_score"            "SG_dbNSFP(dbNSFP_2.0)_2_PolyPhen2_HDIV_score"  "SG_dbNSFP(dbNSFP_2.0)_2_PolyPhen2_HDIV_pred"   "SG_dbNSFP(dbNSFP_2.0)_2_PolyPhen2_HVAR_score" 
[25] "SG_dbNSFP(dbNSFP_2.0)_2_PolyPhen2_HVAR_pred"   "SG_dbNSFP(dbNSFP_2.0)_2_LRT_score"             "SG_dbNSFP(dbNSFP_2.0)_2_LRT_pred"              "SG_dbNSFP(dbNSFP_2.0)_2_Mutation_Taster_score"
[29] "SG_dbNSFP(dbNSFP_2.0)_2_Mutation_Taster_pred"  "SG_dbNSFP(dbNSFP_2.0)_2_GERP_NR"               "SG_dbNSFP(dbNSFP_2.0)_2_GERP_RS"               "SG_dbNSFP(dbNSFP_2.0)_2_PhyloP"               
[33] "SG_dbNSFP(dbNSFP_2.0)_2_29way_logOdds"         "SG_dbNSFP(dbNSFP_2.0)_2_LRT_Omega"             "SG_dbNSFP(dbNSFP_2.0)_2_1000Gp1_AF"            "SG_dbNSFP(dbNSFP_2.0)_2_1000Gp1_AFR_AF"       
[37] "SG_dbNSFP(dbNSFP_2.0)_2_1000Gp1_EUR_AF"        "SG_dbNSFP(dbNSFP_2.0)_2_1000Gp1_AMR_AF"        "SG_dbNSFP(dbNSFP_2.0)_2_1000Gp1_ASN_AF"        "SG_dbNSFP(dbNSFP_2.0)_2_ESP5400_AA_AF"        
[41] "SG_dbNSFP(dbNSFP_2.0)_2_ESP5400_EA_AF

Note that fields [19:41] are in small caps, which match the header of the vcfF. However, the field descriptors in the info section of the vcfF are all in upper case, e.g.:

NS=1;DP=1196;AF=0.048;SGACOV=58;SGASCORE=0.000;SGGENEDIR=-;SGANNOT=CDS;SGREFAA=G;SGAAC=E;SGMRNAID=8;SGCDSID=7;SGTI=NM_005235.2;SGPI=NP_005226.1;SGGI=ERBB4;SGSEGDES=NT_005403__1..84213159__Genome_Sequence__Chr2;SGSEGPOS=62796652;SGAMBGAINPEN=0.000;SGAMBLOSSPEN=0.000;SG_DBNSFP(DBNSFP_2.0)_2_SIFT_SCORE=0.0300;NA;SG_DBNSFP(DBNSFP_2.0)_2_POLYPHEN2_HDIV_SCORE=1.0000;0.9810;0.9990;NA;SG_DBNSFP(DBNSFP_2.0)_2_POLYPHEN2_HDIV_PRED=D;.;SG_DBNSFP(DBNSFP_2.0)_2_POLYPHEN2_HVAR_SCORE=1.0000;0.7430;0.8600;NA;SG_DBNSFP(DBNSFP_2.0)_2_POLYPHEN2_HVAR_PRED=D;P;.;SG_DBNSFP(DBNSFP_2.0)_2_LRT_SCORE=0.0000;NA;SG_DBNSFP(DBNSFP_2.0)_2_LRT_PRED=D;.;SG_DBNSFP(DBNSFP_2.0)_2_MUTATION_TASTER_SCORE=NA;SG_DBNSFP(DBNSFP_2.0)_2_MUTATION_TASTER_PRED=.;SG_DBNSFP(DBNSFP_2.0)_2_GERP_NR=5.8300;SG_DBNSFP(DBNSFP_2.0)_2_GERP_RS=5.8300;SG_DBNSFP(DBNSFP_2.0)_2_PHYLOP=2.7610;SG_DBNSFP(DBNSFP_2.0)_2_29WAY_LOGODDS=20.1150;SG_DBNSFP(DBNSFP_2.0)_2_LRT_OMEGA=0.0000;NA;SG_DBNSFP(DBNSFP_2.0)_2_1000GP1_AF=NA;SG_DBNSFP(DBNSFP_2.0)_2_1000GP1_AFR_AF=NA;SG_DBNSFP(DBNSFP_2.0)_2_1000GP1_EUR_AF=NA;SG_DBNSFP(DBNSFP_2.0)_2_1000GP1_AMR_AF=NA;SG_DBNSFP(DBNSFP_2.0)_2_1000GP1_ASN_AF=NA;SG_DBNSFP(DBNSFP_2.0)_2_ESP5400_AA_AF=NA;SG_DBNSFP(DBNSFP_2.0)_2_ESP5400_EA_AF=NA

Not surprisingly, when the fields don't match exactly, we get all NA:

> info(readVcf(vcfF,'hg19'))[55,c(1:4,20:23)]
DataFrame with 1 row and 8 columns
                       NS        DP            AF        SGACOV SG_Cosmic(Cosmic_68)_68_COSMIC_Count SG_dbNSFP(dbNSFP_2.0)_2_SIFT_score SG_dbNSFP(dbNSFP_2.0)_2_PolyPhen2_HDIV_score
                <integer> <integer> <NumericList> <IntegerList>                            <integer>                          <numeric>                                    <numeric>
2:212587234_C/T         1      1196         0.048            58                                   NA                                 NA                                           NA
                SG_dbNSFP(dbNSFP_2.0)_2_PolyPhen2_HDIV_pred
                                                <character>
2:212587234_C/T                                          NA​


Any ideas on how to overcome this problem with the vcf file?
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] VariantAnnotation_1.12.4 Rsamtools_1.18.2         Biostrings_2.34.0        XVector_0.6.0            GenomicRanges_1.18.3     GenomeInfoDb_1.2.3       IRanges_2.0.0            S4Vectors_0.4.0         
 [9] Biobase_2.26.0           BiocGenerics_0.12.1      ROC_1.42.0               sva_3.12.0               genefilter_1.48.1        mgcv_1.8-3               nlme_3.1-118             BiocInstaller_1.16.1    
[17] data.table_1.9.4        

loaded via a namespace (and not attached):
 [1] annotate_1.44.0         AnnotationDbi_1.28.1    base64enc_0.1-2         BatchJobs_1.5           BBmisc_1.8              BiocParallel_1.0.0      biomaRt_2.22.0          bitops_1.0-6           
 [9] brew_1.0-6              BSgenome_1.34.0         checkmate_1.5.0         chron_2.3-45            codetools_0.2-9         DBI_0.3.1               digest_0.6.4            fail_1.2               
[17] foreach_1.4.2           GenomicAlignments_1.2.1 GenomicFeatures_1.18.2  grid_3.1.2              iterators_1.0.7         lattice_0.20-29         Matrix_1.1-4            plyr_1.8.1             
[25] Rcpp_0.11.3             RCurl_1.95-4.3          reshape2_1.4            RSQLite_1.0.0           rtracklayer_1.26.2      sendmailR_1.2-1         splines_3.1.2           stringr_0.6.2          
[33] survival_2.37-7         tools_3.1.2             XML_3.98-1.1            xtable_1.7-4            zlibbioc_1.12.0   
annotation vcf readvcf variantannotation • 1.2k views
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0
Entering edit mode
jls2282 • 0
@jls2282-7127
Last seen 5.4 years ago
United States

OK, maybe not the most elegant solution, but here is code that fixes the vcf header on a vcfF file:

 

#Find 1st header block
library(data.table)
row=1
while(substr(fread(vcfF,nrows = 1,skip=row-1,header = F,sep="\n"),1,6)!="##INFO"){
  row=row+1
}
first row<-row
header1<-fread(vcfF,nrows=firstrow-1,header=F,sep='\n')
#Find INFO block
while(substr(fread(vcfF,nrows = 1,skip=row-1,header = F,sep='\n'),1,6)=="##INFO"){
  row=row+1
}
mid row<-row
header2<-data.table(NULL)
for(row in firstrow:(midrow-1)){
  line<-fread(vcfF,nrows=1,skip=row-1,header=F,sep=',')
  line$V1<-toupper(line$V1)
  header2<-c(header2,paste(line,collapse=","))
}
# find last INFO block
row<-midrow
while(substr(fread(vcfF,nrows = 1,skip=row-1,header = F,sep='\n'),1,2)=="##"){
  row=row+1
}
last row<-row
header3<-fread(vcfF,skip=midrow-1,nrows=lastrow-midrow,header=F,sep='\n')
# get tabbed body
body<-fread(vcfF,skip=lastrow-1,header=F,sep='\t')
# write to file
fw<-file(paste0(vcfF,"_fixed"),open = 'wt')
write.table(header1,fw,col.names=F,row.names=F,quote = F)
write.table(unlist(header2),fw,col.names=F,row.names=F,quote = F)
write.table(header3,fw,col.names=F,row.names=F,quote=F)
write.table(body,fw,sep = '\t',col.names = F,row.names=F,quote=F)
close(fw)
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