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ConPair software uses 7387 pre-selected informative genomic markers based on following criteria.
SNVs (easier to genotype from sequencing data)
exonic (to allow comparison of exome and WGS samples…
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Hi @freeseek
Following up on #68, I was wondering if it may be feasible for you to include an Illumina_genotype tag in the FORMAT field? I see that based on ALLELE_A/ALLELE_B and GT the illumina_g…
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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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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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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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There are a number of existing slots/mixins/classes relating to - broadly speaking - phenotypic frequency. Recent discussions suggest room for improvement in their definition, structure and relationsh…
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These were implemented early on, before the schema/variables where standardized. I'm not sure if there's any appetite to update them, but here are a few observations:
- Both use custom methods to c…
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We could support multiple ploidy. A column can only contain one vector, so storing the ploidy information there is difficult. However, we could simply add a ploidy column to the `$fam` slot of the `bi…
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Hi,
I have a few questions related to the phasing options.
1. Why is the default SNP panel limited to these variants: "7.4M SNPs with minor allele frequency (MAF) > 0.05:"? If I have tumor data …
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**Describe the bug**
In the output of `vcfwave`, the phased genotypes are not consistent with the input VCF.
**To Reproduce**
Here are some examples of the incorrect phased genotypes.
Inpu…