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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?

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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.

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  • $\begingroup$ thank you for the response ! $\endgroup$
    – Maryem Life
    Commented May 27, 2022 at 9:42

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