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Total Counts.
If would be great if output of --varlens-allele-support included a column containing the total count for all alleles at a given locus.
| source | contig | interbase_start | interbase_e…
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If a read is rejected for low quality in the remap stage, its paired read never gets matched in the sam2aln stage. Currently, that is not reported, but unmatched reads could easily be added to the `fa…
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Scanning my logs, a good chunk of my failed jobs have something along these lines with a double mutation having an off-by-one location end:
``` python
ValueError: Expected variant 1:109461324 'GG' > …
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Translated sequences should start GSHS
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Figure out if this is a frame shift error in alignment.
Run 130311, see sample 57974A-5 and others.
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@kosoegawa Could you provide a description of your primary use case (intended utilization) for this software? I'd like to update the README.md with it and ensure there is clarity of purpose. Without…
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Richard H. asked for the pipeline score, minimum coverage, and minimum coverage position to be included in the headers when we download a FASTA file from the Micall page.
Let's work on this after the …
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Provide a way for a user to see consensus sequences from the HLA regions for any samples with coverage. They should be able to see it in the browser, or download it to a file.
This is similar to issue…
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Did we decide/discuss the values to provide here?
There was a set of values proposed in the XSD for SimpleAllele see [SimpleAllele XSD](../tree/master/source/main/resources/clingen-xsd/simpleallele…