Error: no samples in vcf file

[Dan]

Hello,

I have a vcf file that I am trying to use to make bed, fam, and bim files. I am using the code:

plink --vcf ~/filtering/test1/outfiles/test1.vcf --make-bed --out ~/filtering/test1/outfiles/test1

And receiving the error:

Error: no samples in .vcf file.

However, when I inspect my vcf file, I see this:

##fileformat=VCFv4.1
##fileDate=20171018
##source=pyRAD.v.3.0.66
##reference=common_allele_at_each_locus
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO            FORMAT  1A_0    1B_0    1C_0    1D_0    2E_0    2F_0    2G_0    2H_0    3I_0    3J_0    3K_0    3L_0

31      20      .       C       G       20      PASS    NS=12;DP=6      GT      1|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0
61      75      .       T       C       20      PASS    NS=12;DP=6      GT      1|1     1|1     1|1     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0
63      71      .       C       T       20      PASS    NS=12;DP=6      GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0     1|1     0|0     0|0     0|0     0|0
89      41      .       A       T       20      PASS    NS=12;DP=6      GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0     1|0     0|0     0|0     0|0     0|0
123     68      .       A       C       20      PASS    NS=12;DP=6      GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     1|0     0|0
145     20      .       A       G       20      PASS    NS=12;DP=6      GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     1|0     0|0     0|0
~                                                                                                                                                                          

If I am not mistaken, everything to the right of FORMAT is a sample, and their genotypes are all listed below. I am not sure why I am receiving samples as I believe the samples are right there?

Thanks so much for your help.

[Dan]

Sorry, I meant: I am not sure why I am receiving a "no samples" error as I believe the samples are right there.

[Christopher Chang]

Hi,

Could you send me
(i) the first few lines of the VCF file, up to the second variant, and
(ii) the .log file from the plink run?

Thanks.

[Dan]

Hi Chris,

Thanks for your help. I have attached the .log file, and here are the first few lines of the VCF file up to the second variant:

##fileformat=VCFv4.1
##fileDate=20171018
##source=pyRAD.v.3.0.66
##reference=common_allele_at_each_locus
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO        FORMAT    1A_0    1B_0    1C_0    1D_0    2E_0    2F_0    2G_0    2H_0    3I_0    3J_0    3K_0    3L_0

31    20    .    C    G    20    PASS    NS=12;DP=6    GT    1|0    0|0    0|0    0|0    0|0    0|0    0|0    0|0    0|0    0|0    0|0    0|0
61    75    .    T    C    20    PASS    NS=12;DP=6    GT    1|1    1|1    1|1    0|0    0|0    0|0    0|0    0|0    0|0    0|0    0|0    0|0

[Christopher Chang]

The main issue is the extra spaces after "INFO" in the last header line; those must be deleted.

You'll also need to decide how you want to translate the IDs. plink's default behavior is to treat '_' as a delimiter between the family ID ("FID") and the individual ID ("IID"), but that doesn't work here since an individual ID of '0' is prohibited. Two simple solutions are "--double-id" and "--const-fid 0"; "--double-id" sets both the FID and IID to the full ID, while "--const-fid 0" sets all FIDs to '0'.

[Dan]

Thank you so much!! I am no longer receiving that error anymore.

I now get an error saying: "Error: invalid chromosome code '31' on line 14 of .vcf file. (This is disallowed for humans. Check if the problem is with your data, or if you forgot to define a different chromosome set with e.g. --chr-set."

However, I saw a fix online suggesting to change all of the chromosome numbers to scaffold numbers (i.e. change 31 to scaffold_31) and then use the option --allow-extra-chr. When I do this, I no longer have errors. Is this the proper way to address this error?

Thanks so much.