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A short question: any programs you recommend for merging TE sites in all samples and genotype the sites in each sample after merging step?
In addition, I have SV data from other programs like Manta, DELLY, etc., do you know how I can merge xTea output with outputs from those programs? (and a program to genotype each sample for list of SVs after merge?).
Thank you in advance,
The text was updated successfully, but these errors were encountered:
dr-ashu-geno
changed the title
Possible to merge TE sites and do genotyping in each sample
Possible to merge TE sites and do genotyping in each sample?
Apr 18, 2024
It's not straightforward to merge with Manta/DELLY output, as they also report some TE insertions in their output. I think the easiest way is to write your own scripts.
Hi.
Thank you for developing xTea.
A short question: any programs you recommend for merging TE sites in all samples and genotype the sites in each sample after merging step?
In addition, I have SV data from other programs like Manta, DELLY, etc., do you know how I can merge xTea output with outputs from those programs? (and a program to genotype each sample for list of SVs after merge?).
Thank you in advance,
The text was updated successfully, but these errors were encountered: