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### Which API Provider are you using?
Ollama
### Which Model are you using?
qwen2.5:32b
### What happened?
Anytime Cline executes a command, the command executes but never returns control back to…
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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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I tried to open a sample file with the openProject command (I renamed this [one ](bcf-examples/Issues_BIMcollab_Example_pr_2018-01-31_17.08.bcf) to sample.bcf) and got the following error. Any idea wh…
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Hello, @odelaneau ,
Thanks for the great work with shapeit5!!
I'm looking into implementing it in a nextflow pipeline (from modules made by @LouisLeNezet, thanks also to him!).
I have a problem…
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I am running bcftools +liftover to convert a vcf file generated with hg19 to hg38
Got these errors/warnings:
Merging 1466 temporary files
[E::hts_open_format] Failed to open file "TempDk63j4/01022.…
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Hello,
I’ve been using hap.py to benchmark two VCF files, but I keep encountering the following warning:
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/IMPORT_FAIL" is invalid, forcing Nu…
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Hi, I'm getting a segfault similar to issue #92, where GLIMPSE_phase (v1.1.1) crashes during or after finalization. This only occurs with haploid data (in fact if I don't provide a `--samples-file` an…
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Hello
For single IFC models, I need to transfer camera information into BCF file. But I see that the coordinate system of BimSurfer and IFC does differ. What can be done to get the correct (according…
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Ubuntu 18.04
htslib 1.15.1-19-g3c44c0b
"liftover" at 1.21-25-g9d314180
80 cpu
512GB RAM
I am attempting to liftover a VCF of ~5 million variants for a single sample. I have tried a BCF, and ind…
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When I try to parse the following xsd:
```
https://github.com/BuildingSMART/BCF-XML/blob/release_2_1/Schemas/visinfo.xsd
```
cxsd fails with the following stack:
```
TypeError: Cannot read…