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Hi Kishwar,
I have just tested PEPPER Nanopore variant calling workflow. My result= is as follows:
##fileformat=VCFv4.2
##FILTER=
##FILTER=
##FILTER=
##FILTER=
##FILTER=
##FORMAT=
##FORMA…
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Example: https://mila.quebec/en/publications/
It would be nice to reuse the same code as in the Mila website. Not sure if that's 'easily' possible via RTD
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Hi,
Maybe this is a silly question but I really don't understand how Allhic can connect contigs from the same haplotype.
For example, in a heterozygous diploid genome, there are two regions on …
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Hello,
I am trying to calculate pairwise differences between sequences from a vcf with missing genotypes.
However, allel.pairwise_distance seems to treat missing genotypes at litteral -1.
Here…
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Hi Haoyu,
This is related to #55, where I noticed that hifiasm was not correctly identifying the heterozygous and homozygous peaks. The animal that I'm working with is very heterozygous (>4%), so t…
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Hi I am new to bioinformatics - I want to be able to identify variants but am confused by the ploidy question in a parasite.
The infecting parasite oocyst has 4 haplotypes However most SNPs I disc…
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thanks a lot
* pvactools version:latest
* Python version:3.7
* Operating System:centos
**Describe the bug**
Failed to compile plugin Wildtype: Excessively long operator at /data/database/anno/…
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I thought the benefit of the dragmap aligner was supposed to be its superior handling of ALT contigs in GRCh38 (compared to bwa mem). But the _--ht-alt-liftover_ option does not look to be supported. …
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Umbrella issue to communicate re development of the [mosquito phasing pipeline](https://github.com/malariagen/pipelines/blob/master/docs/specs/phasing-vector.md). Feel free to raise new issues to deal…
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Hi,
I want to look at some clinical Candida parapsiolosis isolates because I want to make an NxN SNP matrix and MLT. I am use to looking at bacteria and came across this software. I've managed to i…