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AC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF #250

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Emmafei opened this issue Jan 15, 2025 · 0 comments

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@Emmafei
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Emmafei commented Jan 15, 2025

Hi, I encountered an error as follow:
Files:

  • Input region : [chr1:92194902-96096873]
  • Output region : [chr1:93194904-96096873]
  • Reference VCF : [filled_10xquchong.vcf.gz]
  • Output binary : [10x.chr1]

GLIMPSE_split_reference parameters:

  • Sparse MAF : [0.1%]
  • Keep monom. ref sites: [YES]
  • Seed : [15052011]
  • #Threads : [1]

Splitting reference panel:

Parsing specified genomic regions

  • Input region [chr1:92194902-96096873] Output region [chr1:93194904-96096873]
  • VCF/BCF scanning ...
  • VCF/BCF scanning [L=188627 (Lrare= 426 (0.2%) - Lcommon= 188201 - hq= 188201 (99.8%))]
  • VCF/BCF scanning [Nr=140 (Nrh=0 - Nrd=140)]
  • VCF/BCF scanning [Reg=chr1:92194902-96096873 / L=188627] [1.99s]
  • Reference panel parsing ...
    �[31mERROR: �[0mAC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF

and here is my command:
REF=filled_10xquchong.bcf
while IFS="" read -r LINE || [ -n "$LINE" ];
do
printf -v ID "%02d" $(echo $LINE | cut -d" " -f1)
IRG=$(echo $LINE | cut -d" " -f3)
ORG=$(echo $LINE | cut -d" " -f4)
GLIMPSE2_split_reference --reference ${REF} --input-region ${IRG} --output-region ${ORG} --keep-monomorphic-ref-sites --output 10x.chr1
done < chunks.chr1.txt

I tried both bcftools norm -f and bcftools +fill-tags,but not work ,the error remains.
Would appreciate any suggestions, or ideas, thanks!

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