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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

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modified 2 hours ago

written
2 hours ago
by

safiq7130



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