Question: seqVCF2GDS Error Converting VCF to GDS file
0
gravatar for winstondunnmd
10 weeks ago by
winstondunnmd0 wrote:

Dear Bioconductor:

I am a student of SISG Module 17 and used the code to convert my VCF file to GDS file. vcffile <- "data/72S1.vcf.gz" gdsfile <- "data/72S1.gds" seqVCF2GDS(vcffile, gdsfile, fmt.import="GT", storage.option="LZMA_RA", verbose=FALSE)

The VCF file is generated from WES of human, by basespace.illumina.com using the Enrichment App. by Illumina. The VCF file contains a single patient.

I received the following error message.

Error in seqVCF2GDS(vcffile, gdsfile, fmt.import = "GT", storage.option = "LZMARA", : INFO ID 'GMAF' (Number=A) should have 0 value(s), but receives 1. FILE: C:\Users\winst\Documents\data\72S1.vcf.gz LINE: 160, COLUMN: 8, RefMinor;GMAF=C|0.04812;phyloP=-1.165;CSQT=1|DDX11L1|ENST00000456328|downstreamgenevariant,1|WASH7P|ENST00000438504|intronvariant&noncodingtranscriptvariant

Please help.

Winston Dunn

ADD COMMENTlink modified 10 weeks ago by zhengx30 • written 10 weeks ago by winstondunnmd0
Answer: seqVCF2GDS Error Converting VCF to GDS file
1
gravatar for Stephanie M. Gogarten
10 weeks ago by
University of Washington
Stephanie M. Gogarten720 wrote:

seqVCF2GDS is particular about VCF files conforming to the VCF standard. In this case it looks like the header line for "GMAF" has "Number=A", which means there should be one value per alternate allele. The file itself appears to have a row where there is no alternate allele (hence seqVCF2GDS is expecting 0 values), but there is a value provided for "GMAF". You might be able to solve this just by modifying the header, which you can do in the VCF file itself, or by saving a separate file with just the header and modifying that instead. You could then specify that alternate header in seqVCF2GDS:

hdr <- seqVCF_Header("revised_header.vcf")
gdsfile <- seqVCF2GDS(vcffile, gdsfile, header=hdr)
ADD COMMENTlink written 10 weeks ago by Stephanie M. Gogarten720

Thank you Stephanie! The Illumina Basespace provides 2 apps for making the VCF files: the "Enrichment" and "BWA Enrichment" cost exactly the same. When I generated the VCF files with BWA Enrichment it did not cause the problem.

ADD REPLYlink written 10 weeks ago by winstondunnmd0
Answer: seqVCF2GDS Error Converting VCF to GDS file
0
gravatar for zhengx
10 weeks ago by
zhengx30
United States
zhengx30 wrote:

You can directly modify the header in R:

hdr <- seqVCF_Header("data/72S1.vcf.gz")
hdr$info$Number[hdr$info$ID == "GMAF"] <- "."

gdsfile <- seqVCF2GDS(vcffile, gdsfile, header=hdr)
ADD COMMENTlink written 10 weeks ago by zhengx30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 417 users visited in the last hour