Feature request: Parameter to use only control samples to calculate the RUTH stats

[jjfarrell]

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]

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

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On Thu, Nov 7, 2019, 5:24 AM jjfarrell ***@***.***> 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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=ABPY5OOX4J56WLNBILQMBVTQSPUEHA5CNFSM4JKEOBXKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HXR7FCA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABPY5OII35V57V2SYOCRTSLQSPUEHANCNFSM4JKEOBXA> .

[jjfarrell]

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:

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I think this can be addressed when sm-list option works On Thu, Nov 7, 2019, 5:24 AM jjfarrell ***@***.***> 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. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > < #2?email_source=notifications&email_token=ABPY5OOX4J56WLNBILQMBVTQSPUEHA5CNFSM4JKEOBXKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HXR7FCA >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABPY5OII35V57V2SYOCRTSLQSPUEHANCNFSM4JKEOBXA > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=AAO6WDID6IEZB5PCWUVA543QSQLIBA5CNFSM4JKEOBXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDMN3ZQ#issuecomment-551083494>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAO6WDNU6TLG3STKF66MVV3QSQLIBANCNFSM4JKEOBXA> .

-- John Farrell, Ph.D. Biomedical Genetics-Evans 218 Boston University Medical School 72 East Concord Street Boston, MA ph: 617-358-3562 (New Number)

[jjfarrell]

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?