Body: <p>I want to use <a href="https://faculty.washington.edu/browning/conform-gt.html" rel="nofollow noreferrer">conform-gt</a> to get rid of some REF prefix differences see <a href="https://bioinformatics.stackexchange.com/questions/19977/large-amount-of-ref-prefix-differences-after-lifting?noredirect=1#comment29310_19977">here</a>. Conform-gt needs the reference FASTA file split by chromosome and in .vcf.gz format. How can I do this?</p>
  <p>I already tried <code>faidx</code> with</p>
  <pre><code>faidx --transform bed reference/GRCh38_full_analysis_set_plus_decoy_hla.fa &gt; reference/GRCh38_full_analysis_set_plus_decoy_hla.bed
  </code></pre>
  <p>but this produced the following error:</p>
  <pre><code>Traceback (most recent call last):
    File &quot;/home/oem/.local/bin/faidx&quot;, line 8, in &lt;module&gt;
      sys.exit(main())
    File &quot;/home/oem/.local/lib/python3.9/site-packages/pyfaidx/cli.py&quot;, line 202, in main
      write_sequence(args)
    File &quot;/home/oem/.local/lib/python3.9/site-packages/pyfaidx/cli.py&quot;, line 51, in write_sequence
      outfile.write(transform_sequence(args, fasta, name, start, end))
    File &quot;/home/oem/.local/lib/python3.9/site-packages/pyfaidx/cli.py&quot;, line 121, in transform_sequence
      line_len = fasta.faidx.index[name].lenc
  KeyError: 'HLA-A*01'
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-09T18:19:57.780Z
Comments.Text: Can you please [edit] your question and explain what you mean a bit more? Your title talks about converting fasta (sequences) to bed (regions) which is odd, but could be done if you mean "read the fasta and tell me what regions of a reference genome they map to". But then your question talks about converting fasta to "vcf.gz" format and this doesn't make sense unless you want some sort of gVCF file with an entry for every position of a genome.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-09T20:16:53.727Z
Comments.Text: I reconsidered my question. I don't think that I really fully understood what I want to achieve with this format-conversion nor if I really understood what conform-gt really does. Back to the drawing board I guess. I will close this question and hope that the original question in my OP can solve my problem.
Comments.UserDisplayName: mugdi
Tags: <format-conversion><python>
Title: Conversion FASTA to BED fails
ThreadText: # Conversion FASTA to BED fails
  
  (Asked by: username_0 on 2022-11-09)
  
  I want to use [conform-gt](https://faculty.washington.edu/browning/conform-gt.html) to get rid of some REF prefix differences see [here](https://bioinformatics.stackexchange.com/questions/19977/large-amount-of-ref-prefix-differences-after-lifting?noredirect=1#comment29310_19977). Conform-gt needs the reference FASTA file split by chromosome and in .vcf.gz format. How can I do this?
  
  I already tried `faidx` with
  
  ```
  faidx --transform bed reference/GRCh38_full_analysis_set_plus_decoy_hla.fa > reference/GRCh38_full_analysis_set_plus_decoy_hla.bed
  
  ```
  
  but this produced the following error:
  
  ```
  Traceback (most recent call last):
    File "/home/oem/.local/bin/faidx", line 8, in <module>
      sys.exit(main())
    File "/home/oem/.local/lib/python3.9/site-packages/pyfaidx/cli.py", line 202, in main
      write_sequence(args)
    File "/home/oem/.local/lib/python3.9/site-packages/pyfaidx/cli.py", line 51, in write_sequence
      outfile.write(transform_sequence(args, fasta, name, start, end))
    File "/home/oem/.local/lib/python3.9/site-packages/pyfaidx/cli.py", line 121, in transform_sequence
      line_len = fasta.faidx.index[name].lenc
  KeyError: 'HLA-A*01'
  
  ```
  
  **Tags:** format-conversion, python
  
  > **Comments:**
  > **username_1**: Can you please [edit] your question and explain what you mean a bit more? Your title talks about converting fasta (sequences) to bed (regions) which is odd, but could be done if you mean "read the fasta and tell me what regions of a reference genome they map to". But then your question talks about converting fasta to "vcf.gz" format and this doesn't make sense unless you want some sort of gVCF file with an entry for every position of a genome.  
  > **username_0**: I reconsidered my question. I don't think that I really fully understood what I want to achieve with this format-conversion nor if I really understood what conform-gt really does. Back to the drawing board I guess. I will close this question and hope that the original question in my OP can solve my problem.  
  
  ---
  
  ## 0 answers
  
  