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Some DHPS/DHFR joint phenotypes confer S-P/IPTp resistance. Ability to analyse phenotypes across genes jointly would be valuable here, though if there is just this one usecase, it may be easier to jus…
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Hello dear developers,
I have run PECAT on a diploid plant genome (heterozygosity=3.3) and obtained a primary (4.7Gb) and alternate (2.6Gb) set and haplotype1 (4.7Gb) and haplotype2 (2.8Gb). Do yo…
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Hi jannatjiaz,
I am so interested in your ChromoDethripsis methods. I am curious about one issue:
python CTResolveLowDensity.py
--chromosome
--bam
--readnames
--haplotype1_reads
--hapl…
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HapHiC is working very well so far, and now we would like to fine-tune the scaffolding (looking into more of the options, and comparing different input versions).
**My question:** Is it possible t…
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I am getting the above error even though the region is present in my data. What could be wrong?
```bash
./LDBlockShow-1.40/bin/LDBlockShow -InVCF haplotype_gene_quantification/g3_variants/haptags_…
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Post-Shapeit4 vcfdist metrics looked good despite remaining issues with overlapping alleles, suggesting that perhaps vcfdist may not be sensitive to this (or at least not when running in its default m…
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Hi, I mmeet an error like below, I have no idea why this happens, I asked ChatGPT and it told me that in this position, it contains both haploid and diploid genotypes, But I checked the target.vcf fil…
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# nf-core/sarek feature request
## Is your feature request related to a problem? Please describe
Typical effect prediction (SNPEff, VEP) will not take into consideration variants "in phase", i.e…
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When I use --ehh to calculate the EHH curves for the ancestral and derived haplotypes, I think the result is wrong.
e.g. for chrxxx:G:A, In my vcf, allele count for A (derived) is 15 and for G (ances…
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Hello! I am running into an issue with `emase-zero` as implemented in `kbchoi/emase:latest`, getting the error:
`ERROR LOADING TRANSCRIPT LENGTH FILE ; UNKNOWN HAPLOTYPE NAME: PAR`
The issue is th…