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I'm very confused by the implausible results I'm getting on two African American cohorts, one genotyped on an Axiom array and one on an Omni array. For each, I phased them using the Michigan server an…
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I tried imputing gender of samples with guessploidy. In fact I have the gender status of some samples and others I don't have. I used guessploidy on the vcf file and it predicted all the samples to b…
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Expected Behavior
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For Bugs:
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### Environment
#### Steps to Reproduce
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### Description of the bug
Convert GVCF to VCF before validating to reduce the amount of false results
### Command used and terminal output
_No response_
### Relevant files
_No response_
### Sys…
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**Describe the bug**
the "out/final" path didn't have "*.variant_stats.tsv.gz", "*.cell_heteroplasmic_df.tsv.gz", "*.vmr_strand_plot.png" these three files.
**the command code i used is as foll…
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Hello Lindsay,
First of all thank you for your effort putting all these together.
I study a group of aquatics Eriocaulon, and just recently we found out we might have a mix of diploid and polyp…
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The docker used here: https://github.com/broadinstitute/warp/blob/master/tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl#L146 is not public. We should replace it with a public docker.
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Hello mergeBams Team,
Many thanks for the useful tool! With CellRanger v7 intronic reads are included and that might be useful for downstream genotyping. However, do you know if mergeBams includes…
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Hi,
Where can I get more details about the read-through status annotation? I see on the bed file header that the read-through status can be Fusion, ReadThrough, Unannotated, or SenseAntisense. I w…
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is it really 0.08 for all the technologies?
So, whatever Clair3 is fed Pacbio, ont or ilm it can detect SNP present in 8% of the reads? I would have assumed that the detection would work better with…