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Hello,
I am trying to use a variation genome graph to genotype SVs on more samples sequenced with short-reads, and I'm trying different avenues (see 1)graph from vcf + giraffe and 2) graph with pggb+…
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To compare VCFs we can use:
- [x] http://realtimegenomics.com/products/rtg-core-non-commercial/
- [ ] https://github.com/sequencing/hap.py
- [ ] https://github.com/bioinformed/vgraph
- [x] http://smas…
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### Background
VCF files may include a large number of variations and it would be helpful to highlight variants of interest based on INFO field values. NGB shall provide an option to configure set …
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Dear Heng,
I and @gsc74 tried to compare minigraph and Dipcall SV calls by using HG002 HiFi diploid assembly. We used a similar method for comparison as how you had used the Syndip benchmark in the…
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Hi Brad,
I reran the same files with 0.2.1 and received a different set of errors. It again halted during the processing/normalization of the freebayes joint calling file.
If I was only going to use S…
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Hi,
my name is Jordi and I want to use the file svpop-truth-baseline.vcf.gz from https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=vgsv2019/vcfs/
But I dont know how it has …
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I am trying to sanity check HapCUT2 variant calls and validate them using HapCUT2/utilities/calculate_haplotype_statistics.py from (HapCUT2)[https://github.com/vibansal/HapCUT2].
I am taking my Hap…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/202) by Angela Chen (Bitbucket: [AngelaQChen](https://bitbucket.org/AngelaQChen), GitHub: [AngelaQChen](https://github.com/AngelaQChen…
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Hi!
I miss an option to report all sites in VCF outupt, even the ones without genomic variants.
That would allow me to flag potentially non-informative sites, e.g. with low read depth. Application…
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**Steps to reproduce variants not called by RUFUS that are in the gold-standard data set:**
(Notes from S. Gardiner)
Files to reproduce:
So, I've been looking at the RUFUS run from the merged bams o…