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