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Hi,
I use the freebayes to call SNPs and InDels in polypoidy genotype from HiFi aligned bam (120x for haploid genome). And also have the Ultra-long reads aligned bam (reads N50 50kb) 60x. But the b…
baozg updated
3 years ago
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Hi,
I'm new to diploid assemblies and have a few questions about what the different output files represent.
I have a flye assembly with 233 contigs.
After hapdup i have two dual assemblies, one …
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Hello,
I am encountering an issue when running vg autoindex to construct a graph from a HG002 reference FASTA and VCF file. The command I am using is as follows:
vg autoindex --workflow map --thre…
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When I run WhatsHap in vcf + bam (Illumina amplicon sequencing) mode (no pedigree) for data that looks like this:
![image](https://github.com/whatshap/whatshap/assets/1266815/e01b1361-de00-4ed5-ba29-…
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Hi,
Thank you for the nice tool. We recently used HiPhase to phase our Pacbio data and encountered a wired issue. As shown in the below figure, one read with supplementary alignment has two HP tags…
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First of all, thanks so much for developing this great method.
I am working on an extremely rapid tropical tree radiation, and am aiming to infer barriers to gene flow between several co-occurring …
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Hi @aganezov,
I'm trying to merge two assemblies resulted from different settings with Supernova. Since I have fasta file I think I have to convert them in point formatted file by running `fasta2ca…
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Hey Ian,
This is just a thought. I realize that the smith-waterman to both haplotypes helps sort out alignment edge effects with indels, but does it do anything for SNPs? I realize that a nearby in…
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Meta-issue. Please spin out issues and self-assign.
For the first cut, let's organize WDLs and resources for a pipeline that takes
**Inputs**
- the joint short-variant callset
- the integrated…
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CRAM v4 isn't on the cards yet, but it's good to keep track of any ideas in one place so if it ever happens we don't forget something.
- Index format improvements: https://github.com/samtools/hts-spec…