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zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
http://www.bioconductor.org/packages/SNPRelate
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snpgdsOpen error #32

Closed nottwy closed 6 years ago

nottwy commented 6 years ago

The only command I have run was: snpgdsVCF2GDS(merged_snp.fn,"snp.gds",method=c("biallelic.only")) It gave me an error message which said:

Parsing "merged_snp.hard_filtered.vcf" ... Error: Genotype code is out of range "1707194". FILE: merged_snp.hard_filtered.vcf LINE: 1437733, COLUMN: 19, 1707194

So what's wrong with it? 3ku.

zhengxwen commented 6 years ago

It says "1707194" is not a valid genotype. Please check your VCF file (LINE: 1437733, COLUMN: 19).

nottwy commented 6 years ago

I also found there seems to be an I/O problem which causes the format of my vcf to be wrong just now. Thank u for your so quick reply!