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?