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LD score table for East Asians used for BOLT-LMM

I would like to use BOLT-LMM to analyze SNP data of East Asians. The BOLT-LMM requires a table of reference LD scores appropriate for the target ancestry. The LDSC site has various files calculated from 1000 genomes East Asians. (https://console.cloud.google.com/storage/browser/broad-alkesgroup-public-requester-pays) Which one should I use for BOLT-LMM?

For example, I am finding the following files

eas_ldscores
1000G_Phase3_EAS_baseline_v1.1_ldscores
1000G_Phase3_EAS_baseline_v1.2_ldscores
1000G_Phase3_EAS_baselineLD_v2.1_ldscores
1000G_Phase3_EAS_baselineLD_v2.2_ldscores

I would be grateful if you could let me know

bolt-lmm snp ldsc
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updated by LChart LChart • written by Apprentice Apprentice

1 answer

The formats of these files are all the same. The only reason to use any version older than the most recent is to re-produce a result established with the older versions.

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written by LChart LChart

Thank you for your advice. Am I correct in assuming that the relationship is "older < newer" as follows?

eas_ldscores < 1000G_Phase3_EAS_baseline_v1.1_ldscores < 1000G_Phase3_EAS_baseline_v1.2_ldscores < 1000G_Phase3_EAS_baselineLD_v2.1_ldscores < 1000G_Phase3_EAS_baselineLD_v2.2_ldscores

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written by Apprentice Apprentice

That's my assumption. I ignore the un-versioned files since the most likely case (based on other genomics file dumps such as ensembl and ucsc) is that they are the oldest, and the next-most-likely case is that they're updated to always point to the newest versioned file.

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written by LChart LChart

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