<p>If you want the truth VCF, it is <code>full.37m.vcf</code>. <code>rep2.37.broad.hc.raw.vcf.gz</code> is an example call set by GATK.</p>

CC BY-SA 4.0
2022-05-27T09:42:33.020Z
thank you for the response  !
Maryem Life
CC BY-SA 4.0
2022-05-25T03:25:29.337Z
2022-05-25T03:25:29.337Z
user172818
<p>I have a question about syndip dataset : <a href="https://github.com/lh3/CHM-eval" rel="nofollow noreferrer">https://github.com/lh3/CHM-eval</a> .
I'm struggling to find the syndip vcf.</p>
<p>In the release ( <a href="https://github.com/lh3/CHM-eval/releases" rel="nofollow noreferrer">https://github.com/lh3/CHM-eval/releases</a> ), we have a file named : <code>rep2.37.broad.hc.raw.vcf.gz</code>, that i don't know what it is. And we have a file named <code>CHM-evalkit-20180222.tar</code> which contains <code>full.37m.vcf</code> and other files (bed, eval ...).
So i did my search and according to this file: they mentioned that full.37m.vcf is the truth dataset. ( <a href="https://www.biorxiv.org/content/biorxiv/suppl/2018/10/29/456103.DC1/456103-1.pdf" rel="nofollow noreferrer">https://www.biorxiv.org/content/biorxiv/suppl/2018/10/29/456103.DC1/456103-1.pdf</a> Page 16).</p>
<p>The problem is that the file <code>rep2.37.broad.hc.raw.vcf.gz</code> contain variants with <code>MQ, DP, GQ</code> ... that I need to extract. But the <code>full.37m.vcf</code> doesn't contain this information.. ( just <code>Chrom pos ref alt and QUAL</code>.)</p>
<p>So I tried to intersect <code>rep2.37.broad.hc.raw.vcf.gz</code> with <code>full.37m.vcf</code> and take the variant that present in two files, with the DP MQ GQ in <code>rep2.37.broad.hc.raw.vcf.gz</code>.</p>
<p>Is that okay? Since I don't know what is <code>rep2.37.broad.hc.raw.vcf.gz</code>.</p>
<p>And I also noticed that the QUAL in the <code>full.37m.vcf</code> is always 30. Is it normal?</p>

<vcf><public-dataset><variants>
syndip dataset for benchmark variant
# syndip dataset for benchmark variant

(Asked by: username_0 on 2022-05-24)

I have a question about syndip dataset : <https://github.com/lh3/CHM-eval> .
I'm struggling to find the syndip vcf.

In the release ( <https://github.com/lh3/CHM-eval/releases> ), we have a file named : `rep2.37.broad.hc.raw.vcf.gz`, that i don't know what it is. And we have a file named `CHM-evalkit-20180222.tar` which contains `full.37m.vcf` and other files (bed, eval ...).
So i did my search and according to this file: they mentioned that full.37m.vcf is the truth dataset. ( <https://www.biorxiv.org/content/biorxiv/suppl/2018/10/29/456103.DC1/456103-1.pdf> Page 16).

The problem is that the file `rep2.37.broad.hc.raw.vcf.gz` contain variants with `MQ, DP, GQ` ... that I need to extract. But the `full.37m.vcf` doesn't contain this information.. ( just `Chrom pos ref alt and QUAL`.)

So I tried to intersect `rep2.37.broad.hc.raw.vcf.gz` with `full.37m.vcf` and take the variant that present in two files, with the DP MQ GQ in `rep2.37.broad.hc.raw.vcf.gz`.

Is that okay? Since I don't know what is `rep2.37.broad.hc.raw.vcf.gz`.

And I also noticed that the QUAL in the `full.37m.vcf` is always 30. Is it normal?

**Tags:** vcf, public-dataset, variants

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## 1 answers

### Answer by username_1 on 2022-05-25. Score: 1 | Accepted answer

If you want the truth VCF, it is `full.37m.vcf`. `rep2.37.broad.hc.raw.vcf.gz` is an example call set by GATK.

> **Comments:**
> **username_0**: thank you for the response  !  

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