2 hours ago by
Dear All
I am facing a problem to convert the VCF file to .bed file with plink2
first step i update sex information
My Sex information file was like this, I think it is fine.
L63604 1
L63605 2
My phenotype file was like this:(definitely NOT fine)
L56955 eck8
L56956 eck8
L56957 eck8
My command was without Phenotypic data
"plink2 --vcf ZZ_ZW_64_BiSnps.recode.vcf --update-sex SexInfo-M1-F2.txt --chr-set 28 --chr 29,30 --make-bed --out ./ZZ_ZW_64_BiSnps"
My command was withPhenotypic data
"plink2 --vcf ZZ_ZW_64_BiSnps.recode.vcf --update-sex SexInfo-M1-F2.txt --chr-set 28 --chr 29,30 --pheno popInfo-64.txt --make-bed --out ./ZZ_ZW_64_BiSnps"
in the both cases .bed file inside like this (not worked)
UUUUUUu◊}W’W]|UUUUUUUUU’UTUUUWUUˇˇˇˇflˇgfl˝fl˝ˇflˇ˜ˇˇˇˇˇflˇw_˝fi˝ˇflˇ˜ˇU’UUUUUU˝fl˝ˇfløˆˇU’UUUUUU˝€˝ˇflˇ˜ˇUUUUUUUU˝ü˝ˇ ø˜ˇUUUUUUUU˝fl˝ˇfløˆˇUUUUUUUU˝
Second I want to convert VCf file to genpop file, but it is also shows the same.
Command was:
plink2 --vcf ZZ_ZW_64_BiSnps.recode.vcf --chr-set 28 --chr 29,30 --make-pgen -out ./pop-gen/ab
output file was like this:
l l @@6/q!!" r "" !! 1r ! !' 7s7 3""rw""!r!'!A D q1s7 "! 2 @ D 0!r1" 2!!" @[email protected] "D!# """ wrws#" "" 3' DD " $D !" ""7wq7r2'r''ww33s " 7 !"1 ! qG"" !" B ""! r3w" "" 6 $" C t!rw""'q!'[email protected]"r"ww3'" " $ "1 #! #' rr "7$D """ "wBD "r7r'"r "! s3! qw7D D ""wr'' ! r Dq$! ! $! $ r pt "tqw 1! "! wr" 1 "!rD! "! D " ww1'' "D! "[email protected] r" !''
Definitely not worked.
How can overcome this issues. Please please please help
thank you
