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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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Problem in SeqArray::seqVCF2GDS - Parsing the vcf header fails #74

Open iaia87 opened 2 years ago

iaia87 commented 2 years ago

Erreur dans AsDataFrame(s[i], c(T = "ID", T = "Number", T = "Type", T = "Description", : No 'ID'. Parsing the VCF header fails.

I don't know why I have this error, I create my vcf with SeqArray. I think that I have a problem in my header, but how to resolve that ?

I have looked in the github repository, but I don't find out the answer.

Here you are a little vision of the header in terminal window :

fileformat=VCFv4.2

fileDate=20211109

source=SeqArray_Format_v1.0

INFO=<>

INFO=<>

FILTER=

FORMAT=

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DEPAOUKW00002_DEPAOUKW00002 DEPAOUKW00003_DEPAOUKW00003 DEPAOUKW00005_DEPAOUKW00005 DEPAOUKW00008_DEPAOUKW00008 DEP

AOUKW00009_DEPAOUKW00009 DEPAOUKW00011_DEPAOUKW00011 [.....] 21 14625201 21:14625201:T:C T C 100 PASS filter=PASS GT 0/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 [.....]

Thanks for your help and for the package, I really enjoy ! Laura

zhengxwen commented 2 years ago

The line ##INFO=<> should be removed. It is not a standard format.

iaia87 commented 2 years ago

Thanks a lot !

I will try and I will tell you !

Have a good day, Laura