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Dear BubbleGun team,
I believe that there is a bug in the “BubbleGun bchains” command when the option “--fasta” is used.
Bellow, I illustrate this potential bug with a specific example, using t…
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New term request Liver biopsy: inclusion bodies (f444): Hepatic biopsy
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Hello Kimberly, Daniela and Valerio
I’ve been thinking about how to make it clear to the authors what exactly we mean by a disease model paper. Some authors get it but some still flag a paper for h…
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Dear Monarch team,
For a project I finished last year I had to access your API for fetching associations given a set of biological entities. This project relied on the use of predicates that cannot…
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Covers ensuring all HLA typings are valid.
p groups, g groups, single alleles, and multiple allele strings can be verified against the nomenclature directly.
first field XX codes for an invalid …
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Hi there, firstly, congratulations on the excellent toolkit. I've run a test case using the COLO829 sample set.
If I wanted to plot some copy-number plots manually, using HMF-generated copy ratio …
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### Description of the bug
I'm running the singularity version of the tool on a CentOS 7 Linux cluster. Every time I attempt to run it, whether directly via calling "nextflow run..." or via submittin…
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Hi hmftools team,
firstly thank you for developing LILAC tool to detect HLA genotype and LOH. I try to deploy this tool in my series. According to the protocol, I successfully run it on normal sam…
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root@3ca21770deb6:/sequencing/Deepvariant# hiphase --reference pbr.v1.1.chr.fasta --bam Whangkeumbae_sorted.bam --vcf whangk
uembae.vcf.gz --output-vcf whangkeumbae.phased.vcf
[2024-05-27T01:41:46.6…
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Hi,
I've noticed that when using dbNSFP to output prediction scores for polyphen and SIFT, it will output multiple '&' seperated scores (e.g. 1.0&1.0 or 1.0&.) for a single variant. This makes post…