ldsc_users

Contact owners and managers

1–30 of 252

LDSC (LD Score regression) user group

github.com/bulik/ldsc/

Post here with

1. Bug reports.

2. Feature requests (no promises).

3. Questions/comments about documentation (we will try to rewrite confusing bits).

3. Questions about methods/ papers/ stats/ interpretation of results.

0 selected

qser...@gmail.com

9/27/21

LD Hub moved or down?

Hello, could someone please advise if LD Hub has been moved? I tried http://ldsc.broadinstitute.org/

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LD Hub moved or down?

Hello, could someone please advise if LD Hub has been moved? I tried http://ldsc.broadinstitute.org/

9/27/21

Degang WU, … T Wu12

3/30/21

What is "delta method" in the supplementary notes of "LD Score regression distinguishes confounding from polygenicity in genome-wide association ....

A bit of progress here. According to Ghosh 1966, the 2nd moment of sample correlation coefficient can

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What is "delta method" in the supplementary notes of "LD Score regression distinguishes confounding from polygenicity in genome-wide association ....

A bit of progress here. According to Ghosh 1966, the 2nd moment of sample correlation coefficient can

3/30/21

kpric...@gmail.com

12/10/20

Linear mixed model SNP h2

Hi, I have a small sib-pair sample I did a GWAS on. I used linear mixed model and PC's. The fixed

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Linear mixed model SNP h2

Hi, I have a small sib-pair sample I did a GWAS on. I used linear mixed model and PC's. The fixed

12/10/20

Nils Kappelmann

3/10/20

European Reference Panel

Dear LDSC team, I couldn't figure out from the documentation on the European reference panel that

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European Reference Panel

Dear LDSC team, I couldn't figure out from the documentation on the European reference panel that

3/10/20

Peter Hickey2

2/11/20

Running LDSC with GRCh38/hg38 annotations

Bump. Is the Google Group still active or is there somewhere/someone else I might ask? Thanks, Pete

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Running LDSC with GRCh38/hg38 annotations

Bump. Is the Google Group still active or is there somewhere/someone else I might ask? Thanks, Pete

2/11/20

Apprentice

1/20/20

N for each of cases and controls or a total N?

Hi, I am working with a case-control study data, which has a high ratio of controls to cases (eg 5:1)

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N for each of cases and controls or a total N?

Hi, I am working with a case-control study data, which has a high ratio of controls to cases (eg 5:1)

1/20/20

Jiayi Xu

12/9/19

Question about the reference panel and # of SNPs used to estimate heritability.

Hi LDSC support group, I have been trying to estimate a phenotype heritability using its GWAS summary

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Question about the reference panel and # of SNPs used to estimate heritability.

Hi LDSC support group, I have been trying to estimate a phenotype heritability using its GWAS summary

12/9/19

Nils Kappelmann

11/25/19

Genetic Correlation - Confidence Intervals

Dear LDSC team, I was wondering how you would compute confidence intervals from LDSC genetic

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Genetic Correlation - Confidence Intervals

Dear LDSC team, I was wondering how you would compute confidence intervals from LDSC genetic

11/25/19

Kaitlyn Price

11/25/19

R2 for LD partitioning regression

Hi, I used LD partitioning on annotation files I made. I get the coefficient and p-value, but would

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R2 for LD partitioning regression

Hi, I used LD partitioning on annotation files I made. I get the coefficient and p-value, but would

11/25/19

Gabriëlla Blokland, … gao chuan4

11/11/19

LDSC on genotypeXsex interaction betas

Hi, I'm also thinking to apply LDSC on GxE interaction results. Any updates from people? Thanks

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LDSC on genotypeXsex interaction betas

Hi, I'm also thinking to apply LDSC on GxE interaction results. Any updates from people? Thanks

11/11/19

Shi Song RONG

11/6/19

Summary outcomes as "+"/"-" to dummy outcomes?

Hello ldsc group, I just started using ldsc. In one of my GWAS summary datasets, the outcome was

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Summary outcomes as "+"/"-" to dummy outcomes?

Hello ldsc group, I just started using ldsc. In one of my GWAS summary datasets, the outcome was

11/6/19

Michel Nivard

10/2/19

(fully) shared controls

I have 2 GWAS, which fully share their controls, but the sets of cases are unique. Are there known

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(fully) shared controls

I have 2 GWAS, which fully share their controls, but the sets of cases are unique. Are there known

10/2/19

filippo abbondanza

9/16/19

Issues with Genetic correlation

Hi, I'm running some genetic correlation test using LDSC with my traits of interest (two

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Issues with Genetic correlation

Hi, I'm running some genetic correlation test using LDSC with my traits of interest (two

9/16/19

filippo abbondanza

9/6/19

Genetic correlation issue

Hi, I have done GWASs on handedness and I wanted to compute h2 and the genetic correlation with

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Genetic correlation issue

Hi, I have done GWASs on handedness and I wanted to compute h2 and the genetic correlation with

9/6/19

R Reynolds, Jory Schossau13

8/20/19

Can't find baseline model v1.2 in alkesgroup repository

Hi Jory, Apologies for such a delayed response. You understood me correctly. That is, I intend to

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Can't find baseline model v1.2 in alkesgroup repository

Hi Jory, Apologies for such a delayed response. You understood me correctly. That is, I intend to

8/20/19

Melissa Gymrek, Benjamin Neale3

8/13/19

Ignore annotations when performing LD score regression

Got it, thanks for the clarification! ~Melissa On Wed, Aug 7, 2019 at 6:04 AM Benjamin Neale <

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Ignore annotations when performing LD score regression

Got it, thanks for the clarification! ~Melissa On Wed, Aug 7, 2019 at 6:04 AM Benjamin Neale <

8/13/19

Gloria Novikova, Kaitlyn Price2

8/6/19

Appropriate statistical test for LD Score enrichments

Hi, Did you ever figure out the answer to this question? I would like to convert my LD partition

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Appropriate statistical test for LD Score enrichments

Hi, Did you ever figure out the answer to this question? I would like to convert my LD partition

8/6/19

JZ, … Jory Schossau5

7/31/19

hg38 version of both baseline annotation and LD scores

I'm still putting a bow on my workflow for arbitrary population sets and baselines, but a couple

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hg38 version of both baseline annotation and LD scores

I'm still putting a bow on my workflow for arbitrary population sets and baselines, but a couple

7/31/19

tmaj...@broadinstitute.org, … Koen5

7/25/19

LD Scores for custom annotations not matching baseline model SNPs

Hi Paul, I was wondering if you have any scripts available to reprocess the BED files? Best, Koen Op

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LD Scores for custom annotations not matching baseline model SNPs

Hi Paul, I was wondering if you have any scripts available to reprocess the BED files? Best, Koen Op

7/25/19

Jonathan Chung

7/25/19

Generating specifically expressed gene sets for LDSC-CTS

Hello, I would like to apply the cell type enrichment analysis described in the Finucane, 2018 paper

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Generating specifically expressed gene sets for LDSC-CTS

Hello, I would like to apply the cell type enrichment analysis described in the Finucane, 2018 paper

7/25/19

Fei Yangf

7/22/19

big change for rg and gencov after using --no- intercept

Hi ldsc developer, After using no-intercept in our case to calculate the genetic correlation, we

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big change for rg and gencov after using --no- intercept

Hi ldsc developer, After using no-intercept in our case to calculate the genetic correlation, we

7/22/19

Camellia Sarkar, Jory Schossau2

7/11/19

Query regarding partition heritability

Hi Camellia, I haven't used that particular feature myself, but I would guess your parameter

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Query regarding partition heritability

Hi Camellia, I haven't used that particular feature myself, but I would guess your parameter

7/11/19

Daniel Richard, Jory Schossau4

6/27/19

Inability to generate custom-annotation files.

Hi Daniel, I'm unsure exactly what the error is getting at, but I suspect it's because of

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Inability to generate custom-annotation files.

Hi Daniel, I'm unsure exactly what the error is getting at, but I suspect it's because of

6/27/19

Jory Schossau

6/26/19

ValueError: Do you really want to compute whole-chromosome LD Score? (no! I don't think...)

Hi, I'm using custom data (my own hg38 baseline, and constructed annotation files to match), but

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ValueError: Do you really want to compute whole-chromosome LD Score? (no! I don't think...)

Hi, I'm using custom data (my own hg38 baseline, and constructed annotation files to match), but

6/26/19

Yanyu Liang

6/3/19

Get coefficient SD and p-value

Hi developers, I am using stratified LDSC regression and I am wondering if there is an option to

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Get coefficient SD and p-value

Hi developers, I am using stratified LDSC regression and I am wondering if there is an option to

6/3/19

Ying Liu

4/10/19

How correct beta from intercept, and error "Could not determine N"

Sorry if I have newbie questions. My summary statistics have a column A1_CT (varies by SNPs) which

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How correct beta from intercept, and error "Could not determine N"

Sorry if I have newbie questions. My summary statistics have a column A1_CT (varies by SNPs) which

4/10/19

Patrick Sullivan

4/8/19

partitioned LDSC error

Hi - ran into a cryptic error - not a python or numpy user so need a bit of help in trying to figure

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partitioned LDSC error

Hi - ran into a cryptic error - not a python or numpy user so need a bit of help in trying to figure

4/8/19

Sophie Chick

4/8/19

Including p-value for munge_sumstats

Hi, basic question sorry. I'm intending to run some genetic correlations on LD Hub and the data

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Including p-value for munge_sumstats

Hi, basic question sorry. I'm intending to run some genetic correlations on LD Hub and the data

4/8/19

Alex Gileta, … Raymond Walters6

3/29/19

LD Score calculation in non-human system, no genetic map

Hello again. After a long hiatus, our lab is revisiting this question, but this time with an updated

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LD Score calculation in non-human system, no genetic map

Hello again. After a long hiatus, our lab is revisiting this question, but this time with an updated

3/29/19

George

2/22/19

genetic correlations with complete sample overlap

Hi, I have two traits with complete sample overlap (N1=5983,N3=6089). The LDsc intercept is low ~1.01

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genetic correlations with complete sample overlap

Hi, I have two traits with complete sample overlap (N1=5983,N3=6089). The LDsc intercept is low ~1.01

2/22/19