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I am trying to calculate heritability and getting this error:
Call:
./ldsc.py \
--h2 hearta.sumstats.gz \
--ref-ld-chr aCM/Add_all.chr3 \
--out aCM--print-coefficients \
--overlap-annot \
--f…
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Hi, thank you for the iLDSC. Trying it on a sumstat.gz that works for LDSC, returns the index out of range error. and I am using the following syntax.
Any suggestions, would be greatly appreciated.
…
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I am try to generate LD scores using below command
./ldsc.py \
--ref-ld-chr LDSCORE.1000G_AFR.tab.gz \
--out FG_T2D24 \
--rg FG.sumstats.gz,T2D_EUR.sumstats.gz \
--w-ld-chr LDSCORE.1000G_AFR.ta…
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Hi,
I am getting an error running cell type specific regressions as described in https://github.com/bulik/ldsc/wiki/Cell-type-specific-analyses but using my own data.
I get: 'IndexError: list index …
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I am trying to calculate heritability and getting this error:
Reading regression weight LD Score from baselineLD_v2.3/baselineLD.[1-22] ... (ldscore_fromlist)
Traceback (most recent call last):
…
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Hi,
is there difference between '--w-ld-chr' and '--ref-ld-chr'? As the inputs of these two arguments in the example code are same (eur_w_ld_chr), I also pass ld score of reference to the '--w-ld-chr…
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Hello,
I am trying to calcualate heritbaility and I am getting this issue. May I know how to resolve this?
Code:
python3 dsc.py --h2 sbp_hapmap.sumstats.gz --ref-ld-chr eur_w_ld_chr/ --w-ld-…
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I am getting memory error when generating LDscores;
./ldsc.py --bfile "/dataE/AWIGenGWAS/shared/imputed_data_plink/all_imputed_map_qc" --chunk-size 500000 --l2 --ld-wind-cm 1 --out Awi-gen-LDscore…
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The link to Cell type specific analyses reference files do not seem to work
(https://data.broadinstitute.org/alkesgroup/LDSCORE/LDSC_SEG_ldscores/)
Is there an alternate link?
Thanks
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To date the `tree` build dependency must be removed to build the package and `pybedtools` is not available for `win-64` therefore tests are failing. I am currently setting the project platforms to ["l…