<p>It sounds like you want <code>samtools faidx foo.fa</code> followed by <code>samtools faidx foo.fa chr1 &gt; your_subset_file.fa</code> (or whatever the first chromosome is). The output file is then a regular fasta file subset as you like. You can get any chromosome you want with that. In fact, you can also do regions (e.g., <code>chr1:100-1000</code>, though note that the sequence name in the resulting fasta output will be <code>chr1:100-1000</code>, which may break some downstream tools).</p>

CC BY-SA 4.0
2023-12-03T00:16:11.497Z
'samtools faidx foo.fa chr1 > your_subset_file.fa' seems problematic for downstream analysis, specifically ipdSummary doesn't work with the resulted fasta file, and it seems the header is not saved correctly.
Marjan
CC BY-SA 4.0
2023-12-03T08:39:46.193Z
Then that's likely a bug in ipdSummary.
Devon Ryan
CC BY-SA 3.0
2018-01-25T15:24:06.563Z
2018-01-25T15:49:52.400Z
2018-01-25T15:49:52.400Z
Devon Ryan
<p>I have the GATK FASTA reference for hg19. I would like to subset this based on the first chromosome. Normally what I do is open the FASTA as a text file, and then delete all other chromosomes except chromosome 1. </p>

<p>That's awful. </p>

<p>Picard tools has an <a href="https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_fasta_FastaReferenceMaker.php" rel="nofollow noreferrer">option</a>. But this doesn't appear to subset only by chromosome. How could this be done efficiently? </p>

<fasta><reference-genome><picard>
How can I subset a reference based on only the first chromosome?
# How can I subset a reference based on only the first chromosome?

(Asked by: username_0 on 2018-01-25)

I have the GATK FASTA reference for hg19. I would like to subset this based on the first chromosome. Normally what I do is open the FASTA as a text file, and then delete all other chromosomes except chromosome 1.

That's awful.

Picard tools has an [option](https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_fasta_FastaReferenceMaker.php). But this doesn't appear to subset only by chromosome. How could this be done efficiently?

**Tags:** fasta, reference-genome, picard

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## 1 answers

### Answer by username_1 on 2018-01-25. Score: 3 | Accepted answer

It sounds like you want `samtools faidx foo.fa` followed by `samtools faidx foo.fa chr1 > your_subset_file.fa` (or whatever the first chromosome is). The output file is then a regular fasta file subset as you like. You can get any chromosome you want with that. In fact, you can also do regions (e.g., `chr1:100-1000`, though note that the sequence name in the resulting fasta output will be `chr1:100-1000`, which may break some downstream tools).

> **Comments:**
> **username_2**: 'samtools faidx foo.fa chr1 > your_subset_file.fa' seems problematic for downstream analysis, specifically ipdSummary doesn't work with the resulted fasta file, and it seems the header is not saved correctly.  
> **username_1**: Then that's likely a bug in ipdSummary.  

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