somalier
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brentp
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Hi, I'm trying to run somalier to infer relatedness between a large sample of WES datasets (in VCF format). This dataset has roughly 30k samples and 800 SNPs and I'm...
This is a great tool -- thanks for developing and sharing with the community. Using the precompiled binaries for somalier I'm not able to read directly from s3. I've verified...
Do you have any recommendations on dealing with a low number of sites (n)? When it's 0, the relatedness is NaN. When it's a very low number (less than 20),...
Dear all, would it be possible to get more detailed per-site info for QC? Right now somalier outputs only per sample and pairs of samples info. There is already something...
This might be more of a request for clarification than an actual issue or problem with the code. I noticed that the definition of relatedness seem to have changed with...
Hi, I am running the module on a set of samples. The first part up until the .tsv generated ran fine. It took a bit longer than an hour I...
Hi, I'm wondering if one can use gnomad instead of 1k-genomes for the ancestry estimate. somalier files for thousand genomes are restricted to only 5 superpopulations whereas gnomad has a...
https://www.biorxiv.org/content/10.1101/2020.02.11.941773v2 for each of the ~17K snps, we can look for 3 haplotypes (when input is bam/cram). maybe @hannespetur could weigh in on whether this is likely to be enough...
I get the following error when I run somalier relate on about 1000 exomes. Even exomes that are likely from the same individual are being flagged as "unrelated" (possibly because...
