BOLT-LMM error ERROR: 6:63979:C:T has Phased = 2 (not 0)

Question

[Sharad]

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

Answer 1

[Sharad]

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

[Ram]

1. Thank you for following up - please accept your own answer to mark the post resolved.
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