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instead of downstream in the counts subworkflow
Homozygotes aren't useful in allele-specific analyses, so we discard them in the _counts_ subworkflow. But discarding them upstream, even before runn…
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Since the introduction of multiple allele designations for a locus with version 1.8, we could now link specific designations to sequence tags.
Reported by: kjolley
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@iskandr:
> PGV relies on allele-specific quantification of expression from RNAseq, how can that data be shown in Cycledash?
from https://github.com/hammerlab/cycledash/issues/852
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it would make it a lot easier to install with the allele specific expression pipeline
and it really shouldn't be too hard, considering the few number of dependencies WASP has
the challenge will …
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Hi @zhanxw,
Is it possible to specify specific variants in each group (for example epacts format like), other than just specify by range? It's better to have chr:pos:ref:alt like format to have th…
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This is a rather specific idea, but one that, as far as I know, is not well implemented in R. Effective population size (Ne) gives an estimate of the number of individuals that contribute alleles into…
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There are some pipelines that only make sense to run given some conditions which in some cases can be automatically detected through the results of other pipelines.
For example, if you wish to automa…
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So we can change allele freq in the founders (not setting to 0.5 and not estimating from the data)
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Update the PGT FORMAT header as discussed in #6937:
PGT format field on each genotype can be interpreted as being an indicator of which of the two phased haplotypes in the sample contains the site-…
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Hi,
is there currently a way to quantify allele-specific counts at the level of genomic _regions_ rather than individual SNVs? If not, would you consider adding such a feature to a future version o…