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In your instruction:
"For human genome alignment using the GRCh37 build, we recommend using the annotations/ceph18.b37.include.2014-01-15.bed windows to parallelize variant calling (speedseq var and …
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Hello,Professor
I have `HiFi + HiC, Nanopore + HiC data`
The draft assembly of `HiFi data` was finished by `Hifiasm`, draft assembly of` Nanopore data` was finished by `Nextdenova` and the resulti…
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Dear,
I 'm new for de novo mutation. And I read the paper, Prevalence and architecture of de novo mutations in developmental disorders. And I think it's amazing. Could you please help me to lear…
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Is it possible to use CHM13 as a reference for AnnotSV? Even if current annotations are just lifted from GRCh38 to CHM13 it would be very useful. Thank you!
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Thank you for sharing the code. I really appreciate it.
I have a few questions:
1) how do you define SUNK using Jellyfish (I assume)?
2) what does `parentRead` here https://github.com/glogsdon1/su…
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despite #262
we are still seeing some false inversions in regions of CNV, e.g.:
https://legumeinfo.org/gcv2/gene;lis=phavu.Phvul.003G002400?algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&thr…
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Hi,
`whatshap` has phased my vcf files, but I am wondering how to infer break points(crossover or gene conversion) based on the phased haplotypes.
I found `duoHMM` [here](https://mathgen.stats.…
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Hi,
After running EG with v4.2.4 for a while without major problems, we upgraded to 4.4.0 recently and have a couple issues.
It seems one issue is with TEstrainer where run time explodes into we…
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Hey there,
I'm exploring using verkko to assemble some relatively large satellites and segmental duplications in a targeted fashion.
Since the typical HiFi reads + UL reads haven't been sufficie…
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I am using `Version: 0.1.2` of `speedseq` and `version: v0.1.4` of `svtyper`
I have 3 bam files aligned with `bwa mem` to the hg38 reference. This is my speedseq command
```
speedseq sv \
-B …