I have been using "WhatsHap"(https://whatshap.readthedocs.io/en/latest/index.html) tool for haplotype phasing.

And it had been working very well.

Actually, that is the problem.

In the tutorial page,

The basic command-line for running WhatsHap is this:

whatshap phase -o phased.vcf --reference=reference.fasta input.vcf input.bam

I have tried this command line and the results were good.

The output VCF file has phasing information about 'paternal | maternal' (0|1, 1|0, 1|1)

But I don't understand that the input was just VCF file and BAM file of the offspring.

I didn't add any pedigree data or VCF, BAM file of parents.

(The tool has pedigree options too.)

Also, when I check the IGV to see if the 'paternal | maternal' information was correct, it was correct.

How can this happen?