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Hi Jana,
Previously I thought PanGenie only worked with SNPs, insertions, and deletions. However, I read about a study with your contribution (https://doi.org/10.1101/2021.12.20.472354 , "Haplotype…
Sunhh updated
11 months ago
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Hi there,
I've been struggling to fix an error with your tool RE: missed pHF data. It seems numbat only pHF data for chromosomes 1-2 and filters all other SNPs - probably due to all cM values for o…
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Hi
Manta has three variants file:diploidSV.vcf.gz ,candidateSV.vcf.gz and candidateSmallIndels.vcf.gz
so ,should i merge the corresponding which file type(candidateSV.vcf.gz ? discard diploidSV.vcf.…
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If I want to genotype SNPs, InDels and SVs, should I create two indexs, one for SNPs and InDels, and another for SVs, then run kage genotype twice?
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Migrated from https://redmine.open-bio.org/issues/2643 filed by Marco Dall'Olio on 2008-11-06, originally titled "Proposal: fastPhaseOutputIO for SeqIO"
> Hi,
> fastPHASE is software for haplotype…
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Clonal Hematopoiesis, but it's too tricky to spell. :)
**Here's how we are going to do this:**
Rough idea: we swap the TN labels, do unmatched variant calling on the normal, then genotype the tu…
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i'm getting this error while building avocado
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] avocado: A Variant Caller, Dis…
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I would like to impute the data of another chip in order to get the missing points of the BovineSNP50 chip.
My source data in ped format. I got VCF files using plink1.9 and prepared a reference (~500…
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Hello,
As an experiment, I've tried take the vcf of the draft human pangenome, use bcftools +setGT to unphase the pangenome vcf, and then rephase the vcf using different reference panels. I am usin…
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Hello, creators of VADT!
Thank you for creating this tool!
I've been able to successfully run VADT on a test dataset provided with the program, however when I use it on my data it either fails…