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Hello,
I'm running into an issue with running HAPCUT2 with a particular VCF. The extractHAIRS process runs smoothly, but HAPCUT2 gives the following output (file paths omitted):
[2018:04:18 15:5…
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Hi,
First of all, thank you very much for this very flexible tool to phase variants!
I am trying to use HapCUT2 to phase variants in a diploid genome combining Hi-C and Pacbio data. I am not sure …
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/135) by madhubioinfo (Bitbucket: [madhubioinfo](https://bitbucket.org/madhubioinfo), GitHub: [madhubioinfo](https://github.com/madhubi…
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Why am I getting a seg fault?
On this basic data file:
```
1 530673 530672 AAAG
1 2621645 2090972 AAAG
1 19804316 17182671 AAAG
1 22466822 2662506 GAGA
1 22915237 448415 GAGA
1 2304851…
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Hi, everyone.
I was using the msmc2 pipeline to estimate the demographic.
But in my study, the four individuals with a high relatedness at a 1st-degree to 3rd-degree (king software result). So, I…
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I am trying to run nanopolish on my nanopore sequence data, I already finish the following commands:
nanopolish index -d fast5_files/ reads.fasta
canu \
-p ecoli -d outdir genomeSize=4.6m \
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Hi,
I am trying to genotype around 1.2 million STRs across 861 samples.
I'm running HipSTR in parallel (1 CPU per chromosome, total of 23), and it runs fine for some time, but during this step:
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have used HAPCUT before, used reference path directly following --ref, but this time with HAPCUT2/extractHAIRS, keep getting errors as below:
ERROR: Invalid input "--ref" for option flag
also
ERR…
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Hi everyone, if people aren't yet sick of discussing the finer points of GFA implementation, I've got another one! I like the concept of paths in an assembly graph and use them a lot in Bandage, so I'…
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hello,
I am wondering if I could use HapCUT2 to detect misassemblies in my scaffold-level diploid assembly (produced from PE, MP and 10x data by NRGene), in particular with the caveat that I would be…