PLINK requires Sex Info

[maxx694]

Hi

I am trying to analyze vcf file with samples that belong to a cohort. the software came with error which requires to supply sex info because X chromosome is there. However, there is no option to supply this info through vcf2gwas.

`Filtering and converting files

Converting to PLINK BED..
Error: chrX is present in the input file, but no sex information was provided;
rerun this import with --psam or --update-sex. --split-par may also be
`

ignoring chrX and chrY using
bcftools view file.vcf.gz --regions chr14,chr19,chr3,chr16,chr17,chr6,chr5,chr10,chr21,chr18,chr4,chr9,chr1,chr7,chr8,chr20,chr22,chr15,chr12,chr2,chr13,chr11 -o filtered.vcf

solved the issue