fcgene bimbam to plink

Question

[smb2174]

using fcgene software to convert bimbam files into plink format using command line

fcgene --wgd mydosage --pos mymap --oformat plink --out myresult

it seems that reads the dosage file correctly but is given an error

Reading file "mymap":
 EROOR: There should be 5 or 6 columns in each row of file: mymap but this is not the case in 1th row.

according to the software, position file should be a comma delimited file with 3 columns, i.e, example.pos

snp1,  1, 1
snp2,  2, 1
snp3,  3, 1

so that is how the mymap is being formatted

any idea/suggestion?

[Pierre Lindenbaum]

according to the software, position file should be a comma delimited file with 3 column

I cannot find this. Any pointers ?

[smb2174]

Pierre, that is the example that is distributed by the software under a folder called examples/bimbam

[Pierre Lindenbaum]

there is no such folder, I cannot find any example.

$ find fcgene-1.0.7/ -type f -exec grep -lF -- '--pos' '{}' ';'
fcgene-1.0.7/src/cparse.cpp
fcgene-1.0.7/fcgene_static
fcgene-1.0.7/fcgene
fcgene-1.0.7/fcgene.exe

[smb2174]

i still get errors

fcgene --wgd NEWchr22_dosage.txt --geno --pos c22.pos --oformat plink --out c22
EROOR: Are you sure about the argument after --geno? If yes, we suggest you to rename the argument: --pos.

fcgene --wgd NEWchr22_dosage.txt --wbg --pos c22.pos --oformat plink --out c22
EROOR: Are you sure about the argument after --wbg? If yes, we suggest you to rename the argument: --pos

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized. This comment should go under @Pierre's answer.

Answer 1

[Pierre Lindenbaum]

Can you please try:

fcgene --wgd mydosage --geno --pos mymap --oformat plink --out myresult

or

fcgene --wgd mydosage --wbg --pos mymap --oformat plink --out myresult