What is the 'physical phasing'
I wonder about PGT of VCF format field.
According to the meta-information line,
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
I don't know i understood exactly.
If the alleles represent different physical phase, are they in the other strands?
and I found 0|1, 1|0 value in PGT, but I don't know what that mean
I'd appreciate anyone's help. :)
here maybe one literal error
The C alt allele occurs in the chromosome inherited from parent 2 and the G alt allele occurs in the chromosome from parent 2. (Note that which parent is the mother and which is the father is unknown).
which should be parent 1 for one of parent 2
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whynot Two or more variants that are close enough for HaplotypeCaller to attempt to phase share a PID tag. Within a set of variants with the same PID, the PGT tells us which of two homologous chromosomes the alleles fall on. For example, if variants A->C and T->G have PGTs of 0|1 and 1|0, respectively, it means that the alt alleles are out of phase. The C alt allele occurs in the chromosome inherited from parent 2 and the G alt allele occurs in the chromosome from parent 2. (Note that which parent is the mother and which is the father is unknown). If the PGTs were instead both 0|1, the alt alleles would be in phase, occurring on the same parent's copy of the chromosome. If the PGTs were both 1|0 it would mean the same thing, since which parent is considered parent 1 is arbitrary.
The GATK's physical phasing means that we only use one sample and only phase based on co-occurrence of alleles on actual reads. This is in contrast to statistical phasing, which is more powerful and works over much longer ranges but requires multiple samples. That is, the GATK's phasing is not a substitute for a tool like Eagle, but it does give some information about the phasing of rare variants, for example, that a population-based tool would not deal with.
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