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I just tried running the Linux binary of Kindred from https://www.haplotype.org/software.html. It processes a few loci, then segfaults. Nothing is written to the log file.
```
$ ls
kind…
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Good morning,
Our team is currently working to add Pelops to our bioinformatics pipeline. Specifically, we would like to use it within an internally developed tool that currently accepts VCFs and a…
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Hi,
I used:
bcftools mpileup -f reference.fa -b bamlist.txt -r chr10 | bcftools call -m -Oz -f GQ -o chr10-bcf.vcf.gz to get all sites vcf
Then
I used command:
pixy --stats pi dxy fst …
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Unfortunately a new error has come up. It seems similar to previous one with tb-profiler error
[tbprofiler.errlog.txt](https://github.com/user-attachments/files/16063200/tbprofiler.errlog.txt). Again…
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Augur uses a variety of functions to read VCF files, including TreeTime's `read_vcf` which now includes a lot of validation and helpful error messages. We should shift all our VCF reading to use this …
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Hi, thankyou for the amazing set of tools!
I am calling structural variations using GRIDSS, for that I first used SvPrep, then GRIDSS followed by GRIPSS. Then later, I used files generated by GRIPS…
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Hi,
I'm trying to run GraffiTE in the mode that bypasses the SV calling steps but it seems to get stuck at the tsd_prep step. I was wondering if you had any idea why?
```
Loading nextflow/23.04…
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## Describe the issue
Hi,
We are currently using the G2P plugin based on the the global MAF in the locally downloaded gnomAD variants (`gnomADg_r3.1.1_GRCh38` and `gnomADe_r2.1.1_GRCh38`).
The…
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### System
VEP 111 Docker/Singularity
### Full VEP command line
```
singularity exec -H /scratch4/nsobrei2/references/vep_cache_singularity /scratch4/nsobrei2/singularities/vep.sif vep --fork …
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Hello, I'm having difficulty accessing the file referred to in "vcf_path" to create the regional plot with LD information. Could you please share the "1kg_eur_hg19" file with me or provide a link wher…