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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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Error in seqVCF2GDS(vcf.files, gds.file, verbose = FALSE) #76

Open Bulouere opened 2 years ago

Bulouere commented 2 years ago

Hi, I get an error when I'm trying to convert from a vcf file to a gds file using the SeqArray package. Here is my code and the error message.

gds.file <- tempfile() seqVCF2GDS(vcf.files, gds.file, verbose=FALSE) Error in seqVCF2GDS(vcf.files, gds.file, verbose = FALSE) : FORMAT ID 'QSS' (Number=A) should have 1 value(s) but receives 2, please consider revising it to 'Number=.'. FILE: C:\Users\bwodu1\OneDrive - Johns Hopkins\Yegna Lab\u01\test_vcf\55488_60663_Cancer_vs_55488_60664_Benign_mutect2_passed.vcf LINE: 66, COLUMN: 10, 0/1:23,14:0.381

zhengxwen commented 2 years ago

As it said please consider revising it to 'Number=.', please revise the VCF file.