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zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)
http://www.bioconductor.org/packages/SeqArray
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Generate GDS from VCF error #6

Closed cinaljess closed 9 years ago

cinaljess commented 9 years ago

Hello & thanks for the great work. This is similar to previous issue by randomStat. I used GATK to analyze whole genome sequencing data for two samples. I used snpEff for annotation and then used GATK's variantannotator to make the final vcf file. I can send part of the VCF file if you offer. When I try to make a GDS file out of it, I get the following error:

The Variant Call Format (VCF) header: file format: VCFv4.1 the number of sets of chromosomes (ploidy): 2 Parsing "10029667.1.fb.annot.vcf.gz" ... Error: FILE: 10029667.1.fb.annot.vcf.gz LINE: 12599, COLUMN: 8, AC=4;AF=1;AN=4;DB;DP=106;DPB=106;GTI=0;NS=2;NUMALT=1;ODDS=71.5486;PQR=0;PRO=0;QR=0;RO=0;SNPEFF_EFFECT=INTRON;SNPEFF_EXON_ID=6;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=ACOT7;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000361521;SNV;SRF=0;SRP=0;SRR=0;TYPE=snp FILE: fullpath/10029667.1.fb.annot.vcf.gz LINE: 12599, COLUMN: 8, AC=4;AF=1;AN=4;DB;DP=106;DPB=106;GTI=0;NS=2;NUMALT=1;ODDS=71.5486;PQR=0;PRO=0;QR=0;RO=0;SNPEFF_EFFECT=INTRON;SNPEFF_EXON_ID=6;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=ACOT7;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000361521;SNV;SRF=0;SRP=0;SRR=0;TYPE=snp

R_ReplConsole(): before "for(;;)" {main.c}

This is the only error given by R --verbose.

R version 3.1.1 (2014-07-10)

installed.packages() RSQLite NA NA NA "yes" "3.1.1" rtracklayer NA NA NA NA "3.1.1" scales NA NA NA "no" "3.1.1" scatterplot3d NA NA NA "no" "3.1.1" schoolmath NA NA NA NA "3.1.1" sendmailR NA NA NA "no" "3.1.1" SeqArray NA NA NA NA "3.1.1" SeqVarTools NA NA NA NA "3.1.1" ShortRead NA NA NA NA "3.1.1" SparseM NA NA NA "yes" "3.1.1" stringr NA NA NA NA "3.1.1" VariantAnnotation NA NA NA NA "3.1.1" XML NA NA NA "yes" "3.1.1" xtable NA NA NA "no" "3.1.1" XVector NA NA NA NA "3.1.1" zlibbioc NA NA NA NA "3.1.1" base NA NA NA NA "3.1.1" boot NA NA NA "no" "3.1.1" class NA NA NA "yes" "3.1.1" cluster NA NA NA "yes" "3.1.1" codetools NA NA NA "no" "3.1.1" compiler NA NA NA NA "3.1.1" datasets NA NA NA NA "3.1.1" foreign NA NA NA "yes" "3.1.1" graphics NA NA NA NA "3.1.1" grDevices NA NA NA NA "3.1.1" grid NA NA NA NA "3.1.1" KernSmooth NA NA NA "yes" "3.1.1" lattice NA NA NA "yes" "3.1.1" MASS NA NA NA "yes" "3.1.1" Matrix NA NA NA "yes" "3.1.1" methods NA NA NA NA "3.1.1" mgcv NA NA NA "yes" "3.1.1" nlme NA NA NA "yes" "3.1.1" nnet NA NA NA "yes" "3.1.1" parallel NA NA NA NA "3.1.1" rpart NA NA NA "yes" "3.1.1" spatial NA NA NA "yes" "3.1.1" splines NA NA NA NA "3.1.1" stats NA NA NA NA "3.1.1" stats4 NA NA NA NA "3.1.1" survival NA NA NA "yes" "3.1.1" tcltk NA NA NA NA "3.1.1" tools NA NA NA NA "3.1.1" utils NA NA NA NA "3.1.1"

zhengxwen commented 9 years ago

Please send me a part of the VCF file.