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In the g.vcf file, I have the info format of many sample sites that looks like this : 0:0,0:0:99:0,384 (Information corresponding to the GT:AD:DP:GQ:PL). My question is that when 'AD=0 ,DP=0' happe…
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Dear developer:
We used Pangenie to generate population variation genotypes. We found that there were a large number of multi-allelic structural variations in the result file, and most of their diffe…
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Hello,
I am having trouble getting the expected genotyping behaviour from `dysgu run --sites`. I am appreciating help in understanding the problem, which might be a misunderstanding of the expected b…
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Hello,
We're trying to run GenotypeGVCFs on a large genomicsDB workspace. The command is below, with the output. We run these jobs scatter/gather, with each job getting a define, small interval set…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to Bioconductor
Repository: https://github.com/omicscodeathon/rhinotypeR
Confirm the following by edit…
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Hello,
We have a number of short read whole genome sequencing samples (~200) where Aldy is unable to assign a genotype due to low coverage. I was able to successfully run Cyrius and PyPGx on most of …
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Hi @freeseek ,
I dont have the bpm manifest file but I have csv manifest file. Is there any options to convert the idat file to gtc & vcf?
Regards,
Karthick
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When the allele discovery stage runs on large WGS/WES cohorts, the discovered_alleles data structures use a considerable amount of memory not currently accounted for in the `--mem-gbytes` budget. This…
mlin updated
6 months ago
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Hi, I want to convert a large VCF file (~3.5TB) to PLINK ped and map format files. But I got the log file as pasted below:
`Random number seed: 1707568963
773685 MB RAM detected; reserving 386842 …
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Currently we have `-esterrors` and `-estmaf` to estimate genotyping error rate/prob and alternative allele rate/freq/prob. In line with https://github.com/AlphaGenes/AlphaPeel/issues/97 we should use
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