text: user15536: 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?
  
  user37: 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.
  
original_text: 15536: <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>
   37: <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>
  