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For contextual vrs variants do NOT use the clinvar variation name (that is for the canonicalvariation form of the variant. Instead use the hgvs.nucleotide expression which represents the hgvs string t…
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Dear Team
I ran the following pipeline to estimate the CCF of the variants reported in a mutect 2.1 VCF.
The pipeline goes well but in the "sorted_variants.csv" output are printed out only 30000 va…
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Hyperlink to SV in gnomAD/other DBs not appearing correctly. gnomAD doesn't appear at all, and other links are busted.
Links being generated in the form `https://databrowser.researchallofus.org…
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Certain views have gone a bit slow lately - case, variantS come to mind. I haven't dug deep on this, but there are some slow queries I don't quite recognise. They don't look particularly nasty, like p…
dnil updated
11 months ago
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Hi, first of all thanks for this nice tool!
Trying to understand how NGSEP works with a tilling experiment, I tried to reproduce the results of the Gil 2021 paper where the rice tilling population …
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I'd like to request a term for macular retinal dystrophy 1, North Carolina type. This disorder is a little unusual genomically - it is a mutation in a DNaseI hypersensitivity site that affects two gen…
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I've run_clair3.sh etc. with the --gvcf flag. However, when I run the output phased_merge_output.vcf.gz in to gatk CombineGVCFs, I get the following error
A USER ERROR has occurred: The list of …
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Can you set different color for these extension? i don't know how to change it in my hand:
*.bam
*.bai
*.vcf
*.bed
*.R
*.RData
thanks.
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**1)** Right now this handles one variant per case/phenopacket, right? However, will this always be the case for the ERKER format?
How about diseases with autosomal recessive mode of inheritance, whe…
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The primary functions of seqcol are to 1) define unique identifiers for sequencing collections; 2) provide a protocol to serve sequence collection data given the identifiers; and 3) provide a function…