<p>So, columns 7 and 8 should be the genotype of variant 1 (each column is one of the alleles). You have them as 0 1, which means absent and major allele.</p>

<p>I think you're just missing a column. From the doc:</p>

<p>Column 6 is Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric = missing data if case/control)</p>

<p>Ideally you would know which SNPs are heterozygous based on your SNP calling and have such SNPs as 1 2, but if you have a homozygous organism or if you're working with data that's been flattened you can simply generate the .ped file with the same number twice for each SNP.</p>

CC BY-SA 4.0
2020-01-17T14:47:11.733Z
Thanks for your reply. So, I need to phase the data? Because now I have one column per SNP.  I don't have the phenotype column but I specify in the command "--no-pheno"
aguillenea
CC BY-SA 4.0
2020-01-17T15:02:50.447Z
Yeah you're right that --no-pheno should mean it can read them fine, but it says specifically that the first variant in the first column is half-empty. Can you try after adding a phenotype column? You can use -9 to indicate you don't have one.
Thymine
CC BY-SA 4.0
2020-01-17T15:04:53.473Z
Oh, is your example not your real data maybe? I assumed it was real aside from there being more lines and columns
Thymine
CC BY-SA 4.0
2020-01-17T15:07:24.953Z
Actually, it is quite similar to my real data... but I have 5564 individuals (rows) and 46465 SNPs (columns). I will try adding the phenotype column...
aguillenea
CC BY-SA 4.0
2020-01-17T15:15:01.000Z
I have the same error with the phenotype column.
aguillenea
CC BY-SA 4.0
2020-01-17T15:15:23.253Z
On the first line, if you do a cat $file | head -n 1 | awk '{print \$6,\$7}' do you get 0 1? (or 1 0?). Because that's what I think the error message is saying you have
Thymine
CC BY-SA 4.0
2020-01-17T15:24:32.637Z
In my real data, next to the column of phenotypes, I have 0 0 1 0 1 1 1
aguillenea
CC BY-SA 4.0
2020-01-17T15:29:15.887Z
I think that I found the main problem. I should phase the data.
aguillenea
CC BY-SA 4.0
2020-01-17T18:24:06.757Z
No, .ped files do not contain phase information, but they do require *two* columns per variant, and those columns should contain allele codes, not alternate-allele counts.

So, if your first variant is an A/G SNP and your second variant is G/T, columns 6 and 7 of your file should always be "A A", "A G", "G G", or "0 0"; and columns 8 and 9 should always be "G G", "G T", "T T", or "0 0".
Christopher Chang
CC BY-SA 4.0
2020-01-17T14:44:03.237Z
2020-01-17T14:54:12.167Z
2020-01-17T14:54:12.167Z
Thymine
<p>I know that I don't have the correct format in my .ped file for PLINK but I don't know how to convert it.
My actual file is something like:</p>

<pre><code>BSCAN BSCAN20016 0 0 2 0 0 1 1 1....
BSCAN BSCAN20017 0 0 2 0 0 1 1 1....
BSCAN BSCAN20018 0 0 2 0 0 1 1 1....
</code></pre>

<p>Where column 1 is FamilyID, column 2 is ID, column 3 is FatherID, column 4 MotherID, column 5 Sex and then the genotype of each individual.
I only need to create binary files, so I tried to run:</p>

<pre><code>plink-1.9-rc --file admixed --make-bed --no-pheno --cow --out admixed
</code></pre>

<p>but the program shows: Error: half-missing call in .ped file at variant 1, line 1.</p>

<p>Anyone know how can I change the format or recode it to make a correct input?</p>

<p>Thanks in advance!</p>

CC BY-SA 4.0
2023-09-13T16:24:18.647Z
Please consider the response below - its a good response - and consider upvoting/accepting.
M__
<file-formats><plink>
Wrong format .ped in PLINK
# Wrong format .ped in PLINK

(Asked by: username_0 on 2020-01-17)

I know that I don't have the correct format in my .ped file for PLINK but I don't know how to convert it.
My actual file is something like:
BSCAN BSCAN20016 0 0 2 0 0 1 1 1....
BSCAN BSCAN20017 0 0 2 0 0 1 1 1....
BSCAN BSCAN20018 0 0 2 0 0 1 1 1....

Where column 1 is FamilyID, column 2 is ID, column 3 is FatherID, column 4 MotherID, column 5 Sex and then the genotype of each individual.
I only need to create binary files, so I tried to run:
plink-1.9-rc --file admixed --make-bed --no-pheno --cow --out admixed

but the program shows: Error: half-missing call in .ped file at variant 1, line 1.
Anyone know how can I change the format or recode it to make a correct input?
Thanks in advance!

**Tags:** file-formats, plink
> **Comments:**
> **username_1**: Please consider the response below - its a good response - and consider upvoting/accepting.  

---

## 1 answers

### Answer by username_2 on 2020-01-17. Score: 1

So, columns 7 and 8 should be the genotype of variant 1 (each column is one of the alleles). You have them as 0 1, which means absent and major allele.

I think you're just missing a column. From the doc:

Column 6 is Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric = missing data if case/control)

Ideally you would know which SNPs are heterozygous based on your SNP calling and have such SNPs as 1 2, but if you have a homozygous organism or if you're working with data that's been flattened you can simply generate the .ped file with the same number twice for each SNP.

> **Comments:**
> **username_0**: Thanks for your reply. So, I need to phase the data? Because now I have one column per SNP.  I don't have the phenotype column but I specify in the command "--no-pheno"  
> **username_2**: Yeah you're right that --no-pheno should mean it can read them fine, but it says specifically that the first variant in the first column is half-empty. Can you try after adding a phenotype column? You can use -9 to indicate you don't have one.  
> **username_2**: Oh, is your example not your real data maybe? I assumed it was real aside from there being more lines and columns  
> **username_0**: Actually, it is quite similar to my real data... but I have 5564 individuals (rows) and 46465 SNPs (columns). I will try adding the phenotype column...  
> **username_0**: I have the same error with the phenotype column.  
> **username_2**: On the first line, if you do a cat $file | head -n 1 | awk '{print \$6,\$7}' do you get 0 1? (or 1 0?). Because that's what I think the error message is saying you have  
> **username_0**: In my real data, next to the column of phenotypes, I have 0 0 1 0 1 1 1  
> **username_0**: I think that I found the main problem. I should phase the data.  
> **username_3**: No, .ped files do not contain phase information, but they do require *two* columns per variant, and those columns should contain allele codes, not alternate-allele counts.  So, if your first variant is an A/G SNP and your second variant is G/T, columns 6 and 7 of your file should always be "A A", "A G", "G G", or "0 0"; and columns 8 and 9 should always be "G G", "G T", "T T", or "0 0".  

---

