Issues with partitioning Heritability

[Bakhtawar Noor]

I tried partitioning heritability using the following command:

python ldsc.py 
	--h2 BMI.sumstats.gz\
	--ref-ld-chr baseline.\ 
	--w-ld-chr weights.\
	--overlap-annot\
	--frqfile-chr 1000G.mac5eur.\
	--out BMI_baseline

However, I get the following error:

IOError: Could not open baseline.1.l2.ldscore[./gz/bz2]

I've attached the image of the traceback error as well.

And just so you know I have a ldsc folder which I cloned from github. In that I have the folder baseline and in the baseline folder I have files like baseline.16.annot.gz, baseline.16.l2.ldscore.gz, and baseline.16.l2.M_5_50. I have attached the screenshot of baseline folder too. And I am using mac. I would really appreciate if someone can help me in this regard. Thank you in advance.

[Raymond Walters]

Hi,

If I understand your folder structure correctly the problem is that you aren’t specifying the full folder + file stem of the reference files. You probably want something like:

python ldsc.py \

--h2 BMI.sumstats.gz \

--ref-ld-chr ./baseline/baseline. \

--w-ld-chr ./weights_hm3_no_hla/weights. \

--overlap-annot \

--frqfile-chr ./1000G_frq/1000G.acm5eur. \

--out baseline

Cheers,

Raymond

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<Error traceback.png><Screen Shot 2017-10-07 at 12.06.45 PM.png>