File convert vcf to .bed format with plink2

Question

[safiq713]

Dear All

I am facing a problem to convert the VCF file to .bed file with plink2

first step OO update sex information

My Sex information file was like this, I think it is fine.

#IID    SEX
L63604  1
L63605  2

My phenotype file was like this:(definitely NOT fine)

#IID    FAMILY
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 with Phenotypic 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!!" @D@D "D!# """ wrws#" "" 3' DD " $D !" ""7wq7r2'r''ww33s " 7 !"1 ! qG"" !" B ""! r3w" "" 6 $" C t!rw""'q!'!B@rws"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! "AF@ r" !''

Definitely not worked.

How can overcome this issues. Please help

thank you

[Pierre Lindenbaum]

bcftools query -f '%CHROM\t%POS0\t%END\n' in.vcf ?

[safiq713]

It looks like command worked but, I don't get it, how to define Contig, In this data set I have two contig only (Sex chromosomes 29=Z from ZZ and 30=W from ZW)

[W::vcf_parse] Contig '30' is not defined in the header. (Quick workaround: index the file with tabix.)
30  15668   15669
30  15743   15744
30  15795   15796

please help

[Pierre Lindenbaum]

Contig '30' is not defined in the header

the VCF dictionary is missing (lines starting with ##contig= )

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.