mschatz
commented
1 year ago Thanks for your interest!
This file contains the full set of variants: https://bx.bio.jhu.edu/data/jasmine/HG002Trio/DeNovoDetection/denovo.merged.vcf .
It was constructed by merging the results between HG002, HG003, and HG004 across all three technologies. Those in different subsets of technologies can be extracted by filtering on the SUPP_VEC field - for example 100100100 would be those in HG002 only supported by all three techs, 100000000 would be HiFi only, 000100000 would be CLR only, and 000000100 would be ONT only. One note is that this file also includes indel in the range 30-49bp, but filtering out those with SVLEN in the range [-49, 49] would make it SVs only. The plotting script here https://github.com/mkirsche/JasmineFigures/blob/main/figures/jasmine_plot/find_denovo_candidates.R shows examples of extracting these subsets (though this is after the VCF has been converted to a TSV through this script https://github.com/mkirsche/JasmineFigures/blob/main/src/VcfToTsv.java).
Good luck!
Mike & Melanie
On Mon, May 29, 2023 at 9:12 PM Songbo Wang @.***> wrote:
Hi, In your NM paper, you mentioned that your work 'reveals a set of high-confidence de novo SVs confirmed by multiple technologies'. However, I could not find your released SV set. In your data repository ( https://bx.bio.jhu.edu/data/jasmine/), there are several VCFs, but these files contains plenty of SVs. In your Fig. 4, the number of child-only SVs of HG002 on HiFi reads is about 250, where can I find this SV set?
Thanks
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Hi, In your NM paper, you mentioned that your work 'reveals a set of high-confidence de novo SVs confirmed by multiple technologies'. However, I could not find your released SV set. In your data repository (https://bx.bio.jhu.edu/data/jasmine/), there are several VCFs, but these files contains plenty of SVs. In your Fig. 4, the number of child-only SVs of HG002 on HiFi reads is about 250, where can I find this SV set?
Thanks