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srbehera / DRAGEN_Analysis

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dragen_sv_merge.py #1

Closed JosephLalli closed 10 hours ago

JosephLalli commented 11 months ago

Love it.

Do you have dragen_sv_merge.py available for interested individuals? Merging SNP datasets with SV datasets has been trickier than I imagined - it would be lovely if you have a solution!

-Joe

srbehera commented 11 months ago

Hi Joe, We have not merged SNPs with SVs in our analysis. The truvari_merge.sh was used to merge STR, SV and CNVs.

-Sairam

JosephLalli commented 11 months ago

I must have misread, my apologies. At any rate, I would still be interested in seeing the dragen-sv_merge.py code referred to in the truvari_merge.sh script.

srbehera commented 11 months ago

No worries. I am sorry, it seems the dragen-sv_merge.py code is not uploaded. I will take care of that asap. Thanks for noticing that.

srbehera commented 10 months ago

@JosephLalli I have uploaded the dragen_sv_merge.py file. Some additional info can be found on dragen_sv_merge_notes file.

jdidion commented 2 months ago

@srbehera do you still recommend using dragen_sv_merge.py versus truvari collapse?

srbehera commented 2 months ago

@jdidion This script can be used to merge the different type of variant (SV, STR and CNV) vcfs generated by DRAGEN. I think the truvari collapse (https://github.com/ACEnglish/truvari/wiki/collapse) is designed for SV merging.