Left-align reporting multiple alleles at the same position in bacterial genome

[Biltu]

Hello, I have a PGGB pangenome of bacterial isolates, vcf called by vg deconstruct. When I normalized the vcf, multiple alleles were reported for the same POS(554480) and GT(15BCS23). The -f Ref option helps for the other complex regions, so -N is not an option. Is there any other way to correct the POS?

bcftools norm -f ATCC_700669.fasta -m -any \
wave_bub_no_sv.vcf
-Ou |
bcftools view
-e 'COUNT(GT="alt")=0'
-f 'PASS,.'
--threads 8
-Ou |
bcftools sort
-Oz
-o ref_norm_wave_bub_no_sv.vcf.gz

Writing to /var/folders/6m/ymp1jbrj713dr0bg64mwrg2r0000gn/T//bcftools.1nZbbL
Lines total/split/joined/realigned/mismatch_removed/dup_removed/skipped: 80955/1567/0/1169/0/0/0
Merging 1 temporary files
Done
Cleaning
(Swave-env) biltu@Mohammads-MacBook-Pro vcspn % for vcf in wave_bub_no_sv.vcf ref_norm_wave_bub_no_sv.vcf.gz; do
echo
echo "===== $vcf ====="
bcftools query
-f '%CHROM\t%POS\t%ID\t%REF\t%ALT\tAC=%INFO/AC\tAF=%INFO/AF\tAN=%INFO/AN[\t%SAMPLE=%GT]\n'
"$vcf" |
awk -F'\t' '$2==554480 || $2==554481'
done

===== wave_bub_no_sv.vcf =====
NC011900#1#00 554480 >95228>95230 G GAA AC=1 AF=0.0227273 AN=44 10AS22=0 10AS29=0 11ADS26=0 11AS28=0 15AS1=0 15AS10=0 15BCS11=0 15BCS14=0 15BCS19=0 15BCS23=1 15BCS41=0 16FS31=0 18S30=0 18S35=0 18S37=0 18S8=0 19AS15=0 19AS16=0 19AS18=0 19AS2=0 19AS25=0 19AS33=0 19AS34=0 19AS36=0 19AS4=0 19AS40=0 19AS44=0 19AS7=0 29S12=0 35AS27=0 35BS13=0 35BS24=0 35BS38=0 35BS42=0 35BS43=0 35BS5=0 3S39=0 4S9=0 6ABCS17=0 6ABCS20=0 6ABCS21=0 6ABCS3=0 6ABCS6=0 6ABS32=0
NC011900#1#00 554481 >95223>95228_1 A ACTATA AC=1 AF=0.022727 AN=44 10AS22=0 10AS29=0 11ADS26=0 11AS28=0 15AS1=0 15AS10=0 15BCS11=0 15BCS14=0 15BCS19=0 15BCS23=1 15BCS41=0 16FS31=0 18S30=0 18S35=0 18S37=0 18S8=0 19AS15=0 19AS16=0 19AS18=0 19AS2=0 19AS25=0 19AS33=0 19AS34=0 19AS36=0 19AS4=0 19AS40=0 19AS44=0 19AS7=0 29S12=0 35AS27=0 35BS13=0 35BS24=0 35BS38=0 35BS42=0 35BS43=0 35BS5=0 3S39=0 4S9=0 6ABCS17=0 6ABCS20=0 6ABCS21=0 6ABCS3=0 6ABCS6=0 6ABS32=0

===== ref_norm_wave_bub_no_sv.vcf.gz =====
NC011900#1#00 554480 >95228>95230 G GAA AC=1 AF=0.0227273 AN=44 10AS22=0 10AS29=0 11ADS26=0 11AS28=0 15AS1=0 15AS10=0 15BCS11=0 15BCS14=0 15BCS19=0 15BCS23=1 15BCS41=0 16FS31=0 18S30=0 18S35=0 18S37=0 18S8=0 19AS15=0 19AS16=0 19AS18=0 19AS2=0 19AS25=0 19AS33=0 19AS34=0 19AS36=0 19AS4=0 19AS40=0 19AS44=0 19AS7=0 29S12=0 35AS27=0 35BS13=0 35BS24=0 35BS38=0 35BS42=0 35BS43=0 35BS5=0 3S39=0 4S9=0 6ABCS17=0 6ABCS20=0 6ABCS21=0 6ABCS3=0 6ABCS6=0 6ABS32=0
NC011900#1#00 554480 >95223>95228_1 G GACTAT AC=1 AF=0.022727 AN=44 10AS22=0 10AS29=0 11ADS26=0 11AS28=0 15AS1=0 15AS10=0 15BCS11=0 15BCS14=0 15BCS19=0 15BCS23=1 15BCS41=0 16FS31=0 18S30=0 18S35=0 18S37=0 18S8=0 19AS15=0 19AS16=0 19AS18=0 19AS2=0 19AS25=0 19AS33=0 19AS34=0 19AS36=0 19AS4=0 19AS40=0 19AS44=0 19AS7=0 29S12=0 35AS27=0 35BS13=0 35BS24=0 35BS38=0 35BS42=0 35BS43=0 35BS5=0 3S39=0 4S9=0 6ABCS17=0 6ABCS20=0 6ABCS21=0 6ABCS3=0 6ABCS6=0 6ABS32=0
(Swave-env) biltu@Mohammads-MacBook-Pro vcspn % bcftools -v
bcftools 1.24
Using htslib 1.23.1
Copyright (C) 2026 Genome Research Ltd.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
(Swave-env) biltu@Mohammads-MacBook-Pro vcspn %