I am trying to make bim bam bed files from a vcf file but i keep getting an cryptic error:
plink --vcf filename.vcf.gz --recode --out test_out
* Unused command line option: --vcf
* Unused command line option: filename.vcf.gz
I tried just using --file and that throws an error I dont know what it means..... i thought maybe it give me that error because i didnt specify I am giving it a vcf.
plink --file finename.vcf.gz --recode --out test
ERROR: A problem with line 1 in [ filename.vcf.gz.ped ] Expecting 5 + 2 * 456042 = 912089 columns, but found 6
I am guessing I need to use the --file flag and put all the genotypes.... how would I put the genotypes from a vcf into a ped file? The samples are all unrelated affected patients so I created my own PED file by: fam id, sample id = sample number mother, father, sex = 0 phenotpe = 2