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Hi everyone,
Can I use this workflow for tumor only variant calling to detect both Somatic and Germline variants? Or should I first run my data with Mutect in tumor only mode and then use varlocira…
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Like discussed in last night's GA4GH call, I'd like to propose opening up discussion on how to include ethnicity in phenopackets 2.0.
My impression from the discussion was that simple enumeration o…
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Dear all,
I simulated a small data set to learn how to use `Sniffles`. This data contains a heterzygous deletion. However, after ran following command, the genotype for this variant is `1/1`. In m…
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I'm opening this up as an issue so that we can look back on results without having to hunt though emails. I will post some results from 1000G below. I think it is nice to be able to look at this using…
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# Scratch pad
hs38 primary assembly of GRCh38 (incl. chromosomes, unplaced and unlocalized contigs) and EBV
hs38a hs38 plus ALT contigs
hs38DH hs38a plus decoy contigs and HLA genes (r…
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We have identified several strains circulating in Brittany (France) based on a BA.2 backbone but carrying a S:L452R substitution. These isolates carry also ORF1ab:S2519P. There are around 150 similar …
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Dear Xianjie,
May I ask a naive question?
In a given SNP region, what are the criteria being used to categorize a cell as WT(0/0), heterozygote(1/0), and homozygote(1/1)?
Are they categorized…
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Hello to the cellsnp-lite team,
I wanted to ask how cellSNP-lite performs the UMI collapsing?
Best regards,
Martin
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Hi there! We are testing clairS-TO with the `--print_ref_calls` option. My question is: what does the RefCall flag mean? Could you further elaborate on it?
I am aware that in other software it can…
sq101 updated
3 months ago