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statgen / ruth

Robust Unified Hardy-Weinberg Equilibrium Test
Apache License 2.0
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Feature request: Parameter to use only control samples to calculate the RUTH stats #2

Open jjfarrell opened 4 years ago

jjfarrell commented 4 years ago

In case-control studies. it would be useful to limit the calculation of the Robust Hardy-Weinberg Equilibrium statistics to just the controls. To specify in the command-line, it would be nice to be able to specify this with a parameter (--controls control.list or --ped file with the affection status). Or just limit the calculation to those ids in the evec file but output all samples in the output.

hyunminkang commented 4 years ago

I think this can be addressed when sm-list option works

On Thu, Nov 7, 2019, 5:24 AM jjfarrell notifications@github.com wrote:

In case-control studies. it would be useful to limit the calculation of the Robust Hardy-Weinberg Equilibrium statistics to just the controls. To specify in the command-line, it would be nice to be able to specify this with a parameter (--controls control.list or --ped file with the affection status). Or just limit the calculation to those ids in the evec file but output all samples in the output.

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jjfarrell commented 4 years ago

It was not clear to be if the sm-list was subletting the VCF so that those in the list would be the only samples in the output vcf or whether the RUTH stats would be based on the sm-list and the output would contain all the original samples.

On Thu, Nov 7, 2019 at 8:41 AM Hyun Min Kang notifications@github.com wrote:

I think this can be addressed when sm-list option works

On Thu, Nov 7, 2019, 5:24 AM jjfarrell notifications@github.com wrote:

In case-control studies. it would be useful to limit the calculation of the Robust Hardy-Weinberg Equilibrium statistics to just the controls. To specify in the command-line, it would be nice to be able to specify this with a parameter (--controls control.list or --ped file with the affection status). Or just limit the calculation to those ids in the evec file but output all samples in the output.

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jjfarrell commented 3 years ago

To run ruth on a subset of samples in the vcf, bcftools can be used to filter and pipe to ruth. Here is an example....

time bcftools view -s ^HG002 adsp5k.cadre.chr$1.norm.ann.pass.vcf.gz |ruth --vcf - --lambda 0 --lrt-em --evec adsp5k.evec --field GT --num-pc 6 --out $VCF_RUTH

@hyunminkang Has there been any progress yet on getting sm-list working?