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Currently bowtie2 is run with the --very-sensitive flag.
This generates a best fitting of all reads, which is ideal for CNV analysis.
This setting is not necessarily ideal for SNP analysis, as it gen…
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A place to dump relevant literature and possibly summaries too.
Tags in the format `[tag_name]` are added below each paper to allow for searching for specific topic.
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Hi,
I m trying to impute HLA in TopMed Imputed data using Michigan Imputation Server. However job fails stating "**Calculating QC Statistics failed**". Also, when I try to impute Michigan Server Impu…
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## Background
`GenBank` format ("GenBank Flat File Format") is a genomic format that describes nucleotide sequences and their protein translations. `GenBank` file (`.genbank`, `.gb`, `.gbk`) is a s…
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I was thinking it would be in one of the mapping or projection classes, but I couldn't find one. I don't want to have to rely on transcript sequence database lookups or the like, but simply provide t…
nh13 updated
2 months ago
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### Background
VCF files may include a large number of variations and it would be helpful to highlight variants of interest based on INFO field values. NGB shall provide an option to configure set …
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**Describe the bug**
This issue is prompted by a query from a user regarding how the variant `NC_000017.10:g.[7576880del;7576883T>G]` ought to be handled. VariantValidator validates allelic variants …
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hi, i run the SNPGenie and got warning like that :
## WARNING: The CDS coordinates for gene Glyma.01G115000.3.Wm82.a2.v1.CDS.2 in the gtf file do not yield a set of complete codons,
## or are abse…
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Hi, oushujun, thank you for develop this great tool for genome repeat annotation. I want to use EDTA to annotate my genome and met an error.
I install EDTA v2.1.3 by mamba with following script ( I…
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Hi
I have read your exhaustive introduction and paper and I think it can be useful for my purpose. My interest is to study Ecoli within-host diversity for each sample. Basically, each sample is a fas…