Remove the `*` ALT Allele Reporting From a g.vcf Before (or After) Genotyping

Start with the reported bcftools merge and bcftools query commands and the provided trio examples. Determine whether removing '' ALT alleles can preserve phased genotypes and upstream deletion information, then verify the behavior on both pre-genotyped gVCFs and genotyped VCFs. Done means a documented or implemented workflow that avoids downstream '' errors without losing relevant phasing.

I have a large scale dataset of WXS .g.vcfs , I do not have the original FASTA files. I would like to genotype these .g.vcfs into vcfs. These vcfs will be used in downstream applications. The issue is that the g.vcfs were created with GATK HaplotypeCaller without the "--disable-spanning-event-genotyping" flag set to true. This means that * SNPs are introduced so that there is a reported "SNP" at a specific site that an upstream INDEL is spanning (INDEL overlapping a SNP) . This is an issue because I am not interested in * genotypes - my understanding is that this information is already stored in the upstream deletion - and the * are not standard IUPAC base annotation and thus triggers errors in many downstream applications.

What is the correct way to get rid of the reporting to these * ALT alleles?

Looking at bcftools merge I noted the -m ** flag, so I tried this first on the VCF after genotyping:

./bcftools merge **-m none,\*\*** --force-single Genotyped_Sample.vcf.gz -Oz -o merged_Genotyped_Sample.vcf.gz

and then on the original, pre-genotyped g.vcf:

./bcftools merge **-m none,\*\*** --force-single Sample.g.vcf.gz -Oz -o merged_Sample.g.vcf.gz

Neither successfully remove the * ALT alleles.....

WHY DONT YOU JUST REMOVE THE SNPS WITH THE * ALT ALLELE?

The only reason I am hesitant to just remove these variants with grep or awk or something is because I am actually working with sequenced trio, which reports variant phasing information. What I noticed with this data is that after I extract a single subject from the trio vcf (which contains 3 subjects, mother, father and child), I have instances where * ALT variants are present, but the phasing information seems to suggest that they are on the allele opposite of the upstream INDEL. Here is an example - starting with variants in trio VCF:

#CHROM  POS      REF     ALT
chr1    154590147  CCG     C
chr1    154590148  CG      C
chr1    154590149  G       *
chr1    154590149  G       C

and then, when I just extract a single subject bcftools query:

#CHROM  POS         REF   ALT     GT
chr1     154590148   CG  C      0|1
chr1     154590149   G   *      1|0
chr1     154590149   G   C      0|1

maybe I can just delete these SNPs, because the * annotation was not build with phasing in mind and this is just an artifact.