<p>I have four vcf files, <code>SNPs_s1.vcf</code>, <code>SNPs_s2.vcf</code>, <code>SNPs_s3.vcf</code>, and <code>SNPs_s4.vcf</code>, which contain information about SNPs. These vcf files were obtained by using the following methods: the initial input files were short-paired reads</p>
<ol>
<li><p>I did mapping with minimap2</p>
<pre><code>./minimap2 -ax sr ref.fa read1.fq.gz read2.fq.gz &gt; aln.sam
</code></pre>
</li>
<li><p>converted to bam file</p>
<pre><code>samtools view -Sb aln.sam &gt; aln.bam
</code></pre>
</li>
<li><p>Sorted the bam file</p>
<pre><code>samtools sort aln.bam &gt; aln_sorted.bam
</code></pre>
</li>
<li><p>created an index file</p>
<pre><code>samtools index aln_sorted.bam
</code></pre>
</li>
<li><p>created an index file of reference</p>
<pre><code>samtools faidx ref.fa
</code></pre>
</li>
<li><p>extracted the raw variants using freebayes</p>
<pre><code>freebayes -f ref.fa aln_sorted.bam &gt; out_var_s1.vcf
</code></pre>
</li>
<li><p>extracted SNPs using vcf tools</p>
<pre><code>vcftools --vcf out_var_s1.vcf --remove-indels --recode \
   --recode-INFO-all --out SNPs_s1.vcf
</code></pre>
</li>
</ol>
<p>I would like to calculate the fixation index (Fst) between <code>SNPs_s1.vcf</code> and <code>SNPs_s2.vcf</code>, <code>SNPs_s1.vcf</code> and <code>SNPs_s3.vcf</code> etc. I attempted to calculate Fst using <code>bcftools</code>, but I have to provide the id list. I tried the code below for that.</p>
<pre><code>bcftools query -l snps_s1.vcf
</code></pre>
<p>The output was &quot;unknown&quot;.</p>
<p>How do I calculate Fst using the above vcf files? Your suggestions would be appreciated.</p>

CC BY-SA 4.0
2023-12-09T09:29:41.757Z
Can you please explain a bit more about Fst, and why you need to calculate it? I'm used to Fst being interpreted as a population statistic, and it doesn't [currently] make sense to me to calculate it for only a few individuals.
gringer
CC BY-SA 4.0
2023-12-09T23:44:05.330Z
@gringer I would like to use Fst to find the genetic diversity between populations. Which method is better for few individuals?
hina
CC BY-SA 4.0
2023-12-10T06:11:39.163Z
Who is asking you to calculate Fst, and why? If you're doing population genetics, you need populations. A few individuals do not make a population, unless it's kākāpō or kakī, or some other similarly endangered species.
gringer
CC BY-SA 4.0
2023-12-10T14:15:48.213Z
The first issue is easy, the name of your sample in your `snps_s1.vcf` is set to `unknown`. You can fix that bit with `sed -i '/^#CHROM/s/unknown/sample1/' snps_s1.vcf`. But gringer's points are the main issue. What are you really trying to do here with only 4 individuals?
terdon
<phylogenetics><vcf><fst>
Fst calculation from VCF files
# Fst calculation from VCF files

(Asked by: username_0 on 2023-12-08)

I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and SNPs_s4.vcf, which contain information about SNPs. These vcf files were obtained by using the following methods: the initial input files were short-paired reads

I did mapping with minimap2
./minimap2 -ax sr ref.fa read1.fq.gz read2.fq.gz > aln.sam


converted to bam file
samtools view -Sb aln.sam > aln.bam


Sorted the bam file
samtools sort aln.bam > aln_sorted.bam


created an index file
samtools index aln_sorted.bam


created an index file of reference
samtools faidx ref.fa


extracted the raw variants using freebayes
freebayes -f ref.fa aln_sorted.bam > out_var_s1.vcf


extracted SNPs using vcf tools
vcftools --vcf out_var_s1.vcf --remove-indels --recode \
   --recode-INFO-all --out SNPs_s1.vcf



I would like to calculate the fixation index (Fst) between SNPs_s1.vcf and SNPs_s2.vcf, SNPs_s1.vcf and SNPs_s3.vcf etc. I attempted to calculate Fst using bcftools, but I have to provide the id list. I tried the code below for that.
bcftools query -l snps_s1.vcf

The output was "unknown".
How do I calculate Fst using the above vcf files? Your suggestions would be appreciated.

**Tags:** phylogenetics, vcf, fst
> **Comments:**
> **username_1**: Can you please explain a bit more about Fst, and why you need to calculate it? I'm used to Fst being interpreted as a population statistic, and it doesn't [currently] make sense to me to calculate it for only a few individuals.  
> **username_0**: @gringer I would like to use Fst to find the genetic diversity between populations. Which method is better for few individuals?  
> **username_1**: Who is asking you to calculate Fst, and why? If you're doing population genetics, you need populations. A few individuals do not make a population, unless it's kākāpō or kakī, or some other similarly endangered species.  
> **username_2**: The first issue is easy, the name of your sample in your `snps_s1.vcf` is set to `unknown`. You can fix that bit with `sed -i '/^#CHROM/s/unknown/sample1/' snps_s1.vcf`. But gringer's points are the main issue. What are you really trying to do here with only 4 individuals?  

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## 0 answers

