Query regarding partition heritability

[Camellia Sarkar]

Hi,

I am trying to partition heritability using your code and tutorial. My files do not have the chromosome number at the end of the filename, but in the middle. On the website, it is written: "If the chromosome number is in the middle of the filename, you can tell ldsc where to insert the chromosome number by using an @ symbol. For example, --ref-ld-chr ld/chr@". Can you please elaborate on how to use it. My files are, for example, annot.1.Network_Genes_ENSEMBL.l2.ldscore.gz, ......., annot.22.Network_Genes_ENSEMBL.l2.ldscore.gz and
annot.1.Network_Genes_ENSEMBL.l2.M_5_50, ......., annot.22.Network_Genes_ENSEMBL.l2.M_5_50.

I need help in writing "--ref-ld-chr ld/chr@" command for my files.

Thanks in advance.

Regards,

Camellia

[Jory Schossau]

Hi Camellia,

I haven't used that particular feature myself, but I would guess your parameter would be if you are running in the same dir as your annot and gz files:
--ref-ld-chr annot.@.Network_Genes_ENSEMBL
ldsc will append .l2.ldscore.gz I believe.

Alternatively, just rename your files to be like their examples so you won't have to use '@'.