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Samclip calculates alignment end position as alignment start position + length of read.
`my $end = $start + length($sam[SAM_SEQ]) - 1;`
This works fine for Illumina data, but often falls short …
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Hi, I am planning to run the complex repeats associated with FAME, kindly help me to create the json file for SAMD12 gene containing the TTTTA and TTTCA repeats. Thanks
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how to completely uninstall masurca?
thank you
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## Feature Request
We have documentation of the workflow now 🎉 See. https://ikim-essen.github.io/uncovar/
But it's still empty 😔 @alethomas, @AKBrueggemann, @lenakinzel and everyone else: Ple…
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Hi, how to deal with multiple variants in a small region, is there a way to combine them to one variant by Pisces or other tools? Attached file describes the situation we find about EGFR exon 19 delet…
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1. Include our published MDS/AML .meta files in the example data set
2. Run the 1000G Illumina Omni 2.5 data set through Genvisis to create imputation ready VCFs
3. Impute to the TOPMed reference pa…
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Dear Qiimer, I know it is common that illumina 16S sequencing does not include primer sequence but it will be nice to have this option to enable it? It is not convenient to using the parameters in spl…
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Hi all,
I am using align_trim.py script to remove primers from the alignment. In me case, we have performed SARS2 amplification with v3 primer set, and then sequenced with illumina (Miseq).
I …
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Need to clarify what some of the columns in `variants_long_table.csv` file indicate.
There's some inconsistencies sometimes, for example: `REF_DP` + `ALT_DP` doesn't add up; for indels, often `REF_D…
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I´m trying to normalize my data from an EPIC array.
The SWAN normalization works fine.
When trying the "illumina" method I always get this warning: Incompatible dataset and normalization method: not…