BOLT-LMM error ERROR: 6:63979:C:T has Phased = 2 (not 0)
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Entering edit mode
6 days ago
Sharad • 0

Hello,

I am running BOLT-LMM 2.3.5 with following conditions

 bolt \
  --bed= bed \
  --bim= bim \
  --fam=fam \
  --bgenFile=chr{1:22}.bgen \
  --sampleFile=chr1.sample \
  --bgenMinINFO=0.3 \
  --phenoFile=phenofile \
  --phenoCol=phenotype \
  --covarFile=phenofile \
  --covarCol=Sex \
  --qCovarCol=PC{1:10} \
  --numThreads=8 \
  --lmm \
  --LDscoresFile=./LDSCORE.1000G_EUR.tab.gz \
  --geneticMapFile=./genetic_map_hg19_withX.txt.gz \
  --statsFile=t1dgc_imputed_bolt.lmm.tab \
  --statsFileBgenSnps=t1dgc_assoc_bolt-lmm.tab \
   2>&1 | tee t1dgc_imputed_bolt-lmm.log

running above lines gave me error at chromosome 6, 9 and 14:

Checking BGEN file chr6.bgen
(with SAMPLE file t1dgc.sample)...
snpBlocks (Mbgen): 2954440
samples (Nbgen): 9630
CompressedSNPBlocks: 1
Layout: 2
first snpID: 
first rsID: 6:63979:C:T
ERROR: 6:63979:C:T has Phased = 2 (not 0)

Checking BGEN file chr9.bgen
(with SAMPLE file t1dgc.sample)...
snpBlocks (Mbgen): 2014806
samples (Nbgen): 9630
CompressedSNPBlocks: 1
Layout: 2
first snpID: 
first rsID: 9:10163:CT:C

Checking BGEN file chr14.bgen
(with SAMPLE file t1dgc.sample)...
snpBlocks (Mbgen): 1525681
samples (Nbgen): 9630
CompressedSNPBlocks: 1
Layout: 2
first snpID: 
first rsID: 14:20000071:A:T
ERROR: 14:20000071:A:T has Phased = 2 (not 0)

when I ran the bolt lmm as follows:

bolt \
  --bed=t1dgc_QC.S6.bed \
  --bim=t1dgc_QC.S6.bim \
  --fam=t1dgc_QC.S6.fam \
  --bgenFile=chr{1,2,3,4,5,7,8,10,11,12,13,15,16,17,18,19,20,21,22}.bgen \
  --sampleFile=t1dgc.sample \
  --bgenMinINFO=0.3 \
  --phenoFile=t1dgc_pheno_4BOLT \
  --phenoCol=T1D_Status \
  --covarFile=t1dgc_pheno_4BOLT \
  --covarCol=Sex \
  --qCovarCol=PC{1:10} \
  --numThreads=8 \
  --lmm \
  --LDscoresFile=./LDSCORE.1000G_EUR.tab.gz \
  --geneticMapFile=./genetic_map_hg19_withX.txt.gz \
  --statsFile=t1dgc_imputed_bolt.lmm.tab \
  --statsFileBgenSnps=t1dgc_assoc_bolt-lmm.tab \
   2>&1 | tee t1dgc_imputed_bolt-lmm.log

it ran but gave error at the following stage

=== Streaming genotypes to compute and write assoc stats at BGEN SNPs ===

BGEN file: chr1.bgen

Read 9630 indivs; using 9630 in filtered PLINK data
snpBlocks (Mbgen): 3718259
samples (Nbgen): 9630
CompressedSNPBlocks: 1
Layout: 2
ERROR: 1:15211:T:G has Phased = 2 (not 0)

these errors have something to do with the.bgen files but i do not know how to fix the issue.

Any help is highly appreciated.

Thanks
Sharad

errors bgen bolt-lmm • 135 views
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Entering edit mode
3 days ago
Sharad • 0

got the answers from creators of BOLT-LMM

for chnum in {10,11,12,13,14,15,16,17,19,20,21,22};
do 
plink2 --vcf chr$chnum.dose.vcf.gz --make-pgen erase-phase --out chr$chnum_rmPhase
plink2 --pfile chr$chnum_rmPhase --export bgen-1.2 bits=8 id-delim=' ' --out chr$chnum
done
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Entering edit mode
  1. Thank you for following up - please accept your own answer to mark the post resolved.
  2. Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.
    code_formatting
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