Entering edit mode
23 months ago
syxsu
•
0
I used PLINK to generate a vcf and want to use vcftools to analyze it. Here is the first several line of the vcf files:
##fileformat=VCFv4.2
##fileDate=20220520
##source=PLINKv1.90
##contig=<ID=0,length=2147483645
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome"
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 14LM0008_14LM0008 14...**
When I run vcftools, I get the error code:
Error: Unknown option: ##fileDate=20220520
After I delete the first several lines, the new error code occurs:
Error: Unknown option: ##POS
Here is my code:
vcftools --vcf $file --keep $list --max-missing 0.8 --hwe 0.1 --relatedness2 --out ${name}maxmissing.vcf
My vcftools version is 0.1.15
I wonder why this will happen.
Have you tried FixVcfHeader yo try to sanity check the VCFs?
what is the output of