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cc: @williamrowell
@tycheleturner observed some impractically large and sparse phase blocks when running `whatshap phase` on a standard 2x150bp Illumina library: the largest phase block is 173.3 Mb…
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## Germline Pipeline
- Only run DV and its subsequent rules with norm samples
- If pairs file (only relevant to the somatic pipeline, i.e. provided --call-somatic), then pull out normal samples…
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add --min_freq arg to build step to be passed to the vcf_to_linear_prg script, for filtering variants in the vcf by allele frequency when constructing the linear PRG
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Dear Samplot Development Team,
I would like to express my gratitude for developing such a valuable tool like Samplot. Your efforts have significantly contributed to the research community, and I tr…
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### Description of the bug
Hi,
This is about the GATK resource bundle but I am opening a bug report here because I encounter this while using this pipeline.
dbSNP138 has the wrong reference alle…
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## Feature request
Since CombineVariants will not be ported, we need equivalent functionality to its ability to annotate "set", ie which callset(s) a site is present in. Here is an excerpt from a t…
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### Description of the bug
I cannot finish the test of haplotypecaller tool on singularity container.
Of course, when I run my germline samples, I obtained the same error.
The pipeline fails on t…
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Hi,
When I'm using the merge function, I lose some SV calls. I made a Manta- and Delly testfile with each 100 SV calls in them. I merge these files with the function: ./SURVIVOR merge ~/Desktop/sam…
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Hi,
I have a following error when running LDJump.
How can I solve this?
```
>LDJump(VCF, chr = CHR, cores = 10, pathLDhat = "/home/samba/Suijitsu_Public/software/LDhat/", pathPhi = "/home/samba/…