Different outputs from **bcftools norm** command using different version of bcftools

[RENXI-NUS]

Dear developers,

I have a problem regarding the different outputs from bcftools norm command using different version of bcftools.

If I use the bcftools version 1.7-2, the ALT column of some rows have two nucleotides separated by comma:

##bcftools_normVersion=1.7+htslib-1.7-2
##bcftools_normCommand=norm -f /mnt/projects/schmidtf/analysis/Radhika/renxi/bin/library/GRCh38.fa -d all -c sx -O v -o using22sentrix_GS_results_from_RX.noIndel.2Alleles.noINDEL.recode.withChr.setref.nodup.vcf using22sentrix_GS_results_from_RX.noIndel.2Alleles.noINDEL.recode.withChr.vcf.gz; Date=Wed Jul  6 04:39:41 2022
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  1_7516  2_8897  3_9715  4_11564 5_NBM27087      6_NBM90222      7_NBM250287     8_P696  9_NBM9001
       10_NBM9017      11_P631 12_7751 13_8813 14_9047 15_9078 16_10550        17_10761        18_11723        19_P213 20_P625 21_9182 22_10712
chr1    817341  rs3131972       A       T,C     .       .       PR      GT      2/2     2/2     2/1     2/2     2/2     2/2     2/2     2/1     2/1     2/1     2/1     2/1
     2/1     2/1     2/2     2/1     2/2     2/1     2/2     2/2     1/1     2/2
chr1    823656  GSA-rs114525117 G       A       .       .       PR      GT      0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/1     0/0     0/1
     0/0     0/0     0/0     0/1     0/0     0/0     0/0     0/0     0/0     0/0
chr1    858952  rs12127425      G       A       .       .       PR      GT      0/0     0/0     0/0     0/0     0/1     0/0     0/0     0/0     0/0     0/1     0/0     0/0
     0/0     0/0     0/1     0/0     0/1     0/0     0/1     1/1     0/0     0/0
chr1    903175  rs4970383       C       T,G     .       .       PR      GT      2/1     2/2     2/1     2/2     2/2     2/1     2/1     2/1     2/2     2/2     2/1     2/1
     2/2     2/2     2/2     2/2     2/2     2/1     2/1     2/1     2/1     2/1

However, if I use the latest version 1.15.1 for analyzing the same input file, the ALT column has only one nucleotide:

##bcftools_normVersion=1.15.1+htslib-1.15.1
##bcftools_normCommand=norm -f /mnt/projects/schmidtf/analysis/Radhika/renxi/bin/library/GRCh38.fa -d all -c sx -O v -o using22sentrix_GS_results_from_RX.noIndel.2Alleles.noINDEL.recode.withChr.setref.nodup.vcf using22sentrix_GS_results_from_RX.noIndel.2Alleles.noINDEL.recode.withChr.vcf.gz; Date=Wed Jul  6 03:16:32 2022
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  1_7516  2_8897  3_9715  4_11564 5_NBM27087      6_NBM90222      7_NBM250287     8_P696  9_NBM9001
       10_NBM9017      11_P631 12_7751 13_8813 14_9047 15_9078 16_10550        17_10761        18_11723        19_P213 20_P625 21_9182 22_10712
chr1    817341  rs3131972       A       T       .       .       PR      GT      0/0     0/0     0/1     0/0     0/0     0/0     0/0     0/1     0/1     0/1     0/1     0/1
     0/1     0/1     0/0     0/1     0/0     0/1     0/0     0/0     1/1     0/0
chr1    823656  GSA-rs114525117 G       A       .       .       PR      GT      0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/1     0/0     0/1
     0/0     0/0     0/0     0/1     0/0     0/0     0/0     0/0     0/0     0/0
chr1    858952  rs12127425      G       A       .       .       PR      GT      0/0     0/0     0/0     0/0     0/1     0/0     0/0     0/0     0/0     0/1     0/0     0/0
     0/0     0/0     0/1     0/0     0/1     0/0     0/1     1/1     0/0     0/0
chr1    903175  rs4970383       C       T       .       .       PR      GT      0/1     0/0     0/1     0/0     0/0     0/1     0/1     0/1     0/0     0/0     0/1     0/1
     0/0     0/0     0/0     0/0     0/0     0/1     0/1     0/1     0/1     0/1

May I ask why there is such a difference? Because the difference will potentially affect downstream analysis results.

Thank you, Ren Xi

[pd3]

Err, can you please provide a small test case to reproduce the problem?