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Hello,
vg giraffe is running quite a bit slower than expected on the HPRC graphs based on the reported numbers. Can you help me debug this problem?
**1. What were you trying to do?**
I woul…
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Hi,
Working with the cactus/vg programs has been really insightful and has produced some very interesting results so far. I'm currently genotypying some short read samples based on known SVs presen…
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As I understand it, the main theoretical benefits of emit statements is that they should make it easier to parallelize a program by ensuring that each element in a set is independent of the others (or…
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When trying to align short reads to the HPRC pangenome, I got a signal 11 error. It works with vg 1.44.0.
I downloaded the HPRC CHM13-based pangenome index from the S3 repo and ran with:
```
wg…
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Hey!
I was trying to build a graph of 400K bacterial genomes and got the following error:
```
terminate called after throwing an instance of 'std::runtime_error'
what(): num_contigs must be l…
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Hi @chfi,
I just got my 2D layout for a human pangenome using `odgi`. Just wondering how can I install `gfaestus` in order to use the interactive tool for navigating the VGS?
Thanks in advance!
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Hello,
I tried to index a human pangenome for giraffe with 'autoindex' and the program crashed.
The command:
```
~/vg_akt/vg autoindex --workflow giraffe -r hs37d5.fa -v chr1.vcf.gz -v chr2.v…
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We built a pan-genome using minigraph-cactus, then converted to vg format and built index files, and everything was fine.
However, I don't have your pantranscriptom.gbwt, pantranscriptom.gbwt. ri an…
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**Overall question**
I was wondering about model choice (i.e., haplotypes, transcripts, or haplotype-transcripts).
**Model choice**
I have RNA-seq data for which the diplotype of each indivi…
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Hello,
I am constructing a human pan genome by pggb from more than 50 haplotyped-resloved genomes according to the [HPRC pipeline ](https://github.com/pangenome/HPRCyear1v2genbank). My command is
…