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Error occurred while processing INFO tag "RPA" when use bcftools merge #2348

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TuBieJun opened this issue Dec 30, 2024 · 1 comment
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@TuBieJun
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I use follow command to merge two vcfs:

bcftools merge 41210352005326.vcf.gz.setgt.vcf.gz 41231210606008.vcf.gz.setgt.vcf.gz -o temp.vcf

Then got the error info:

[W::bcf_hdr_merge] Trying to combine "RPA" tag definitions of different lengths
Error occurred while processing INFO tag "RPA" at 1:10815

I search the position of two vcfs, found nothing strange:

$ bcftools view -H  41210352005326.vcf.gz.setgt.vcf.gz 1:10815
1       10815   rs1205319490    T       TC      103.34  PASS    AC=2;AF=1;AN=2;DP=3;Entropy=0.26;ExcessHet=3.0103;FS=0;GC=78.29;MLEAC=2;MLEAF=1;ML_PROB=0.06;MQ=39;NBQ=25.333;QD=34.45;RPA=1,2;RU=C;ReadPosEndDist=25.667;SOR=1.179;STR;UDP=4        GT:AD:DP:GQ:PL       1/1:0,3:3:9:121,9,0
 bcftools view -H  41231210606008.vcf.gz.setgt.vcf.gz 1:10815
1       10815   rs1205319490    T       TC      244.52  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=1.534;ClippingRankSum=-0;DP=10;Entropy=0.35;ExcessHet=3.0103;FS=0;GC=78.5;MLEAC=1;MLEAF=0.5;ML_PROB=0.08;MQ=43.45;MQ0=0;MQRankSum=-1.534;NBQ=28.455;QD=30.57;RPA=1,2;RU=C;ReadPosEndDist=21.5;ReadPosRankSum=-0.157;SOR=0.595;STR;UDP=10    GT:AD:DP:GQ:PL  1/1:1,7:8:21:257,0,21

The bcftools version info:

$ bcftools version
bcftools 1.20
Using htslib 1.20
Copyright (C) 2024 Genome Research Ltd.
License Expat: The MIT/Expat license
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
@pd3
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pd3 commented Jan 22, 2025

The error message suggests that the tag RPA is defined differently in the header of the input files. The program requires that the definition is the same, use bcftools reheader to fix.

@pd3 pd3 closed this as completed Jan 22, 2025
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