Issue with GWAS-PW: ERROR in segment position (position out of current segment range)

[DaXuanGarden]

Description:

Hi developers and community,

I am using GWAS-PW (v0.21) to analyze two phenotypes, LST and PCOS, but I encountered the following error during execution. The program seems to report an issue about a SNP position being outside the current segment range specified by the BED file.

Command I Used:

/home/daxuan/20240812_RA_CMT_GWAS_omics/14_GWAS_PW/gwas-pw-0.21/src/gwas-pw \
-i ./LST_PCOS_GWAS_PW_input.gz \
-bed /home/daxuan/20240812_RA_CMT_GWAS_omics/14_GWAS_PW/gwas-pw-0.21/example_data/all_fourier_ls.bed \
-phenos LST PCOS

Parameter Settings:

:::Parameter settings::::
:: Input file: ./LST_PCOS_GWAS_PW_input.gz
:: Output stem: gwas-pw
:: Phenotype 1: LST
:: Phenotype 2: PCOS
:: Segment bedfile: /home/daxuan/20240812_RA_CMT_GWAS_omics/14_GWAS_PW/gwas-pw-0.21/example_data/all_fourier_ls.bed
:: V: 0.01 0.1 0.5 
:: Fine-mapping?: no
:: Numbered segments?: no
:: Print: yes
:: MCMC: no
:: Correlation: 0
:: Overlapping cohorts: no
:::::::::::::::::::::::::

Error Output:

ERROR: current segment is 20001200 21131604, position is 20000538

What I Have Tried:

1. Checked chromosome and position consistency:

   • Ensured that the CHR format in the input file matches the BED file (e.g., chr1 vs 1).
   • Verified that the SNP positions (POS) in LST_PCOS_GWAS_PW_input.gz fall within the ranges provided in all_fourier_ls.bed.

2. Validated the BED file:

   • Used the provided all_fourier_ls.bed file from the gwas-pw example data.

3. Filtered input data:

   • Attempted to filter SNPs in LST_PCOS_GWAS_PW_input.gz to ensure all positions fall within the BED file's defined ranges.

However, the error persists, and I am unsure how to proceed further.

Input Data File Info:

• Input file: LST_PCOS_GWAS_PW_input.gz (generated from GWAS summary statistics for LST and PCOS traits)
• BED file: all_fourier_ls.bed (from gwas-pw example data)
• Phenotypes: LST, PCOS

Example line from LST_PCOS_GWAS_PW_input.gz:

SNPID	CHR	POS	Z_LST	V_LST	Z_PCOS	V_PCOS
rs123456	chr1	20000538	2.5	0.02	1.8	0.03

Example line from all_fourier_ls.bed:

chr1	20001200	21131604

My Questions:

1. How can I properly ensure that the SNP positions in my input file align with the BED file's segments?
2. Is there a specific preprocessing step or validation tool recommended for the input files?
3. Could this issue be related to the gwas-pw version or BED file format?

Contact Information:

DaXuan
Email: [email protected]

Thank you for your help!