GRS calculation and merging multiple bed files

[Sue]

Hi Christopher,

I have two questions.

1. First, I have question regarding GRS calculation.

I have bed file as input file (with bim and fam file), and a list of SNP with beta coefficient (here i only had one SNP info in the tsv file).

The command ran right but the result file contains no GRS values.

I'm attaching the log below.

=======================

PLINK v1.90b7.2 64-bit (11 Dec 2023)
Options in effect:
  --bfile /media/user/LaCie/selected_SNPs_for_GRS/vitaminC_snps/chr5_extracted_1
  --out /media/user/LaCie/selected_SNPs_for_GRS/vitaminC_snps/GRS_vitc_chr5_1.txt
  --score /media/user/LaCie/selected_SNPs_for_GRS/vitaminC_snps/vitc_chr5_1_beta.tsv

Hostname: user
Working directory: /home/user/Downloads/plink_linux_x86_64_20231211
Start time: Tue Apr 30 09:53:03 2024

Random number seed: 1714438383
64003 MB RAM detected; reserving 32001 MB for main workspace.
1 variant loaded from .bim file.
72291 people (0 males, 0 females, 72291 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/media/user/LaCie/selected_SNPs_for_GRS/vitaminC_snps/GRS_vitc_chr5_1.txt.nosex
.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 72291 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is exactly 1.
1 variant and 72291 people pass filters and QC.
Note: No phenotypes present.
Error: No valid entries in --score file.

End time: Tue Apr 30 09:53:04 2024

=======================

2. I also have a question regarding a code to merge multiple bed files.

Thank you always,

Sue

[Matthew Maher]

Your log says you only have one variant in your bim/bed.  And even that one was not in your —score input

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[Sue]

Mmm, I checked my bim file and score file(I intended to have one variant in both bed and score file). And the variant in bed and score file matched..

Is there any other way to solve this issue?

2024년 4월 30일 화요일 오전 11시 17분 6초 UTC+9에 mma...@broadinstitute.org님이 작성:

[Matthew Maher]

Bear in mind that 'matching' is done on the variant ID only (col 2 of the BIM).  NOT the CHR, POS, etc.    And the allele code in your score file must be one of the two alleles for the variant in the BIM.

To view this discussion on the web visit https://groups.google.com/d/msgid/plink2-users/86826c5b-7c15-4538-9319-b2695d1390d1n%40googlegroups.com.

[Sue]

I have encountered a challenge with the bim file I possess. The bim files are based on Axiom identifiers rather than rs# identifiers. Unfortunately, I am unable to convert Axiom identifiers to rs#s because the reference is not publicly available.

All I have are the target rs#s for which I wish to calculate the GRS, along with their respective positions. So, I tried matching the position information in the bim file with that in the score file to facilitate the analysis, which seems not right as you advised L

So.. I am seeking advice on how to proceed with analyzing the GRS. Could you kindly provide guidance on the best approach to achieve this?

Thank you for your help!

2024년 4월 30일 화요일 오후 9시 48분 25초 UTC+9에 mma...@broadinstitute.org님이 작성: