PRSice-2 without Ref SNP ID
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4 months ago
Jenish ▴ 20

Does PRSice-2 support a base tile that has chromosome number/name and chromosome position instead of reference SNP ID in the base file?

I'm trying to calculate PRS scores using a weights file from the PGS catalog with ~6 million variants. The file has only chr name and chr positions. Does PRSice-2 support such files as base files? Or, is there a way to get the ref SNP ID in bulk for all the ~6 million variants using the chr name and chr positions?

Catalog PGS PRSice PRS • 413 views
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4 months ago
Lemire ▴ 910

The second point in this FAQ might help:

http://www.prsice.info/faq/

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Thanks for the response. I had completely missed that section out. I was able to calculate the weights using the --chr-id option. Do you know of any other option that needs to be set besides these when generating PRS scores from the weight files?

    --a1 effect_allele \
    --a2 reference_allele \
    --bar-levels 1 \
    --base base_weights.txt \
    --beta  \
    --binary-target T \
    --bp chr_position \
    --chr chr_name \
    --chr-id c:l-ab \
    --fastscore  \
    --no-clump  \
    --no-regress  \
    --out PRSice \
    --pvalue pval \
    --stat effect_weight \
    --target chr#
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