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MCHap can report haplotypes that have not been called in the posterior mode of any individual (i.e., and allele count of 0). This is necessary when reporting statistics over the posterior (such as the…
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## Bug Report
### Affected tool(s) or class(es)
GATK Haplotypecaller
### Affected version(s)
(4.3.0.0 and 4.2.6.1)
### Description
We used Haplotypecaller in GVCF mode (initially in 4.2.…
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Could you please find alternate name shortenings for allelic fraction and allele frequency instead of AF for both?
Thanks :)
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Hello:
I am trying to compare the result using 1kg unphased between plink and emeraLD, and I got totally different result. Also, I found a lot of LD generated by emeraLD have R vale >1 or
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Currently, figuring out what fields are available requires running a command like:
```
gsutil cat gs://gnomad-public/release/2.0.2/vcf/exomes/gnomad.exomes.r2.0.2.sites.vcf.bgz | gunzip -c - | head …
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The function `sgkit.window_by_position` fails if the input dataset has contigs that lack variant sites, throwing an `IndexError`.
Traceback
```python
IndexError …
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_From @jayoung on July 25, 2018 3:5_
hi there,
Me again. I'm not sure if this is a request for help, or a suggestion for an enhancement to Bio::PopGen::Population.
I'm running some McDonald…
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Hi,
I'm trying to run snpgdsIBDMLE function from the SNPRelate package on a seqArray obtained from your example :
file
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**Hi, so sorry to be a bother.
I am analyzing a big autosomal dominant pedigree using Merlin (parametric linkage analysis).
I filtered and extracted markers from chr8 (644 SNPs in total) and prepare…
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Hi there!
I am trying to mtCojo analysis on Alzheimer's Diseases by conditioning on Small vessel disease by running this:
gcta64 \
--mbfile 1000G_EUR_Phase3.mtcojo_ref_data.txt \
--mtcojo-file…