bcftools may be able to help https://samtools.github.io/bcftools/bcftools.html
it has the "F_PASS" filter expression, and you can filter based on different variant types. they list a couple
they list some examples of what you can filter on in their docs
sample genotype: reference (haploid or diploid), alternate (hom or het, haploid or diploid), missing genotype, homozygous, heterozygous, haploid, ref-ref hom, alt-alt hom, ref-alt het, alt-alt het, haploid ref, haploid alt (case-insensitive)
GT="RA" or GT="AR"
GT="Aa" or GT="aA"
possibly this command can filter based on fraction
bcftools view -i 'F_PASS(GT="ref")<0.5' in.vcf
when I see 0/0 genotype for one or several samples in a multi-sample vcf file, does that mean there is no variant identified for that sample/samples?
0/0 means both alleles match the 'reference', so yes, no variant identified for that sample/samples. 0/1 would be that one allele had the variant matching the first entry from ALT. 0/2 would be one allele had a variant match the second entry from ALT.
Format of My VCF file
is there anything about this you want me to check?
Yes, dear cmdcolin; Does the command you suggested work on this file or does it need to be modified? Sorry if my questions are elementary
as far as I can tell, should be fine. i am not a bcftools expert but I'd just try it out and experiment, the filtering expressions are quite powerful with it