<p>I would like to get a pca plot from the multiple sequence alignment (fasta file). I extracted snps in vcf format using snp-sites program.</p>
<pre><code>snp-sites -v -o output.vcf alignment.fasta
</code></pre>
<p>SNPRelate package was used to get a pca plot from the vcf file</p>
<pre class="lang-r prettyprint-override"><code>library(gdsfmt)
library(SNPRelate)

vcf.fn &lt;- &quot;C:/users/downloads/output.vcf&quot;
snpgdsVCF2GDS(vcf.fn, &quot;test.gds&quot;, method=&quot;biallelic.only&quot;)
snpgdsSummary(&quot;test.gds&quot;)

The total number of samples: 266 
The total number of SNPs: 0 
SNP genotypes are stored in SNP-major mode (Sample X SNP)

genofile &lt;- openfn.gds(&quot;test.gds&quot;)
test_pca&lt;-snpgdsPCA(genofile)
Hint: it is suggested to call `snpgdsOpen' to open a SNP GDS file instead of `openfn.gds'.
Principal Component Analysis (PCA) on genotypes:
Excluding 0 SNP on non-autosomes
Error in .InitFile2(cmd = &quot;Principal Component Analysis (PCA) on genotypes:&quot;,  : 
  There is no SNP!
</code></pre>
<p>How do I resolve this error? or Any other methods available to get a PCA plot from the alignment file?</p>

CC BY-SA 4.0
2024-10-07T10:31:06.727Z
What is the error? You have no SNPs in your input so cannot do any analysis on SNPs. For more help, you will need to edit your question and explain what you are doing in more detail. What are you aligning here? Do you have any data in the vcf?
terdon
CC BY-SA 4.0
2024-10-08T00:35:42.183Z
Please show the first few lines of your VCF file, especially the tiles that include genotypes.
gringer
<r><vcf><snp><pca><multi-fasta>
pca plot from multiple sequence alignment
# pca plot from multiple sequence alignment

(Asked by: username_0 on 2024-10-07)

I would like to get a pca plot from the multiple sequence alignment (fasta file). I extracted snps in vcf format using snp-sites program.
snp-sites -v -o output.vcf alignment.fasta

SNPRelate package was used to get a pca plot from the vcf file
library(gdsfmt)
library(SNPRelate)

vcf.fn <- "C:/users/downloads/output.vcf"
snpgdsVCF2GDS(vcf.fn, "test.gds", method="biallelic.only")
snpgdsSummary("test.gds")

The total number of samples: 266 
The total number of SNPs: 0 
SNP genotypes are stored in SNP-major mode (Sample X SNP)

genofile <- openfn.gds("test.gds")
test_pca<-snpgdsPCA(genofile)
Hint: it is suggested to call `snpgdsOpen' to open a SNP GDS file instead of `openfn.gds'.
Principal Component Analysis (PCA) on genotypes:
Excluding 0 SNP on non-autosomes
Error in .InitFile2(cmd = "Principal Component Analysis (PCA) on genotypes:",  : 
  There is no SNP!

How do I resolve this error? or Any other methods available to get a PCA plot from the alignment file?

**Tags:** r, vcf, snp, pca, multi-fasta
> **Comments:**
> **username_1**: What is the error? You have no SNPs in your input so cannot do any analysis on SNPs. For more help, you will need to edit your question and explain what you are doing in more detail. What are you aligning here? Do you have any data in the vcf?  
> **username_2**: Please show the first few lines of your VCF file, especially the tiles that include genotypes.  

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## 0 answers

