Answers.Body: <p>After some guidance from my advisor, this command allowed me to get the output file I needed.</p>
  <pre><code>bcftools view -o newvcfFileName.g.vcf -s 123.2 locationOfTheFile chrom1 chrom2 ... chrom23(mito DNA) --force-samples
  </code></pre>
  <p>I listed every chromosome's title until I typed --force-samples. I found it simpler to copy and paste the names in.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-09-22T17:18:58.923Z
Answers.LastActivityDate: 2023-09-22T17:18:58.923Z
Answers.UserDisplayName: Lauren Sabo
Body: <p>My objective is to take a g.vcf.gz file and from 25-30 unmapped contigs with titles like &quot;NW_020192317.1&quot;, I want to make a subset of ~10k variants from each of the unmapped contigs and make one final g.vcf file that includes the header from the original g.vcf.gz file.</p>
  <p>From the post <a href="https://bioinformatics.stackexchange.com/questions/3565/subset-smaller-bam-to-contain-several-thousand-rows-from-multiple-chromosomes">here</a>, I have tried running:</p>
  <pre><code>samtools view -bo output.g.vcf -s 123.4 inputfile.g.vcf.gz NW_020192317.1
  </code></pre>
  <p>and I keep receiving the output:</p>
  <pre><code>Aborted (core dumped)
  </code></pre>
  <p>I'm not too picky about the number of variants per contig, as long as it is in the thousands, that's why I tried using &quot;.4&quot;</p>
  <p>Alternatively, I tried using the code:</p>
  <pre><code>samtools view input.g.vcf.gz &quot;NW_020192317.1:1-2&quot; &gt; output.g.vcf
  </code></pre>
  <p>and I recieved the same response of &quot;Aborted (core dumped)&quot; with nothing else. I am confused what is wrong here and why it is throwing an error.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-14T20:21:54.747Z
Comments.Text: You at least need to be using bcftools, not samtools, if you are working with vcf files. samtools is designed for bam/sam, not vcf, and that’s why it’s throwing that error
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T08:29:19.337Z
Comments.Text: Do you have a list of contigs of interest? Are those contig names the first field of the VCF? Does this need to be a _random_ selection or can you keep the first 10k variants from each contig?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T13:40:19.570Z
Comments.Text: Also, gvcf files contain both variants non-variant lines. Do you only want variants?
Comments.UserDisplayName: terdon
Tags: <vcf><samtools><gatk><subset>
Title: I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header
ThreadText: # I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header
  
  (Asked by: username_0 on 2023-09-14)
  
  My objective is to take a g.vcf.gz file and from 25-30 unmapped contigs with titles like "NW\_020192317.1", I want to make a subset of ~10k variants from each of the unmapped contigs and make one final g.vcf file that includes the header from the original g.vcf.gz file.
  
  From the post [here](https://bioinformatics.stackexchange.com/questions/3565/subset-smaller-bam-to-contain-several-thousand-rows-from-multiple-chromosomes), I have tried running:
  
  ```
  samtools view -bo output.g.vcf -s 123.4 inputfile.g.vcf.gz NW_020192317.1
  
  ```
  
  and I keep receiving the output:
  
  ```
  Aborted (core dumped)
  
  ```
  
  I'm not too picky about the number of variants per contig, as long as it is in the thousands, that's why I tried using ".4"
  
  Alternatively, I tried using the code:
  
  ```
  samtools view input.g.vcf.gz "NW_020192317.1:1-2" > output.g.vcf
  
  ```
  
  and I recieved the same response of "Aborted (core dumped)" with nothing else. I am confused what is wrong here and why it is throwing an error.
  
  **Tags:** vcf, samtools, gatk, subset
  
  > **Comments:**
  > **username_1**: You at least need to be using bcftools, not samtools, if you are working with vcf files. samtools is designed for bam/sam, not vcf, and that’s why it’s throwing that error  
  > **username_2**: Do you have a list of contigs of interest? Are those contig names the first field of the VCF? Does this need to be a _random_ selection or can you keep the first 10k variants from each contig?  
  > **username_2**: Also, gvcf files contain both variants non-variant lines. Do you only want variants?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2023-09-22. Score: 3
  
  After some guidance from my advisor, this command allowed me to get the output file I needed.
  
  ```
  bcftools view -o newvcfFileName.g.vcf -s 123.2 locationOfTheFile chrom1 chrom2 ... chrom23(mito DNA) --force-samples
  
  ```
  
  I listed every chromosome's title until I typed --force-samples. I found it simpler to copy and paste the names in.
  
  
  ---
  
  