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I was wondering if it's possible to obtain the chromosome and position by idx using pgenlibr, or if it is possible to add this feature?
Thanks so much. The pgenlibr is really useful for an R user…
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Hello,
Thank you for this tool. I am attempting to use this to do power calculations for pan-genome GWAS. These are the commands I have run:
python3 ./scripts/annotate_nodes_newick.py --input_…
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I am using mango-distribution-0.0.1 on Hadoop 2.6.0-cdh5.14.4/spark version 2.2.0/Scala version 2.11.8
Mango submit fails with parquet class not found. I tried to pass parquet class in CLI but it no…
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**TODO**
- [x] Generate table with the following columns {sample name, # variants in primary xls, # of variants in calls xls, # variants imputed, total number of variants in sample}
- [x] Generate…
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@joellembatchou I have a question about the DF=x that shows up in the output file. For the additive test the DF=1 but for GENE_P, SKAT etc. the DF=3..11. But the log10P value is only w.r.t the DF=1. (…
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Check if it still applies:
https://rmagno.eu/gwasrapidd/articles/faq.html#5-genomic-coordinates-of-genomic-contexts-seem-to-be-wrong-
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Hello, I am using selscan to compute iHS with the 1000G 30x data.
About the 1000G 30x data I only used:
- Unrelated individuals (from CEU population)
- Phased and polarized biallelic variants
…
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Currently we have pages for specific variants, but if you want to find variants of interest, you are restricted to either (1) autocomplete searches on label or (2) finding another entity of interest (…
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Please forgive me for my ignorance if this is already implemented - Is there a method to download the mutations of variants through the API? I noticed 2 days ago the download button on lineage reports…
tyhho updated
3 years ago
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Hi,
We are currently using the VEP v111 Docker container to annotate VCF files. However, we are facing the following issues:
1. Performance Issue: Annotation of a very small sample VCF file takes…