Hi, I have genotyped a trio, and then phased them using PhaseByTransmission of GATK Tools. I have then parsed the output vcf file using BCFTools query command. The output file looks like as follows:
#CHR POS FAT MOT CHILD
20 65288 G/T ./. ./.
20 65900 A|A A|G A|A
20 66720 ./. C/A C/A
20 68749 T|C C|C C|T
20 69094 G/A ./. ./.
The phasing information can be interpreted as Mother|Father. Now, I understand that the Child Phasing can be done by applying Mendelian Laws. But How the phasing of Father or Mother is done here? For example here
20 68749 T|C C|C C|T
every person of the trio is phased; even the father (het) without even knowing grand parents of the child. As I am a new researcher in this field, your clarification will help me a lot to understand phasing.
Thank you very much,
-Ruhul
•
written
by
shajib.sust •
1 answer
Yes good point. The child's genotype is MOTHER|FATHER but there is no way GATK would know for GRANDMOTHER|GRANDFATHER for either of the parents. It's just a custom to use '|' for the whole trio if the child is phased.
Log in to answer this question.
-
Trio de novo analyses
written by jan
-
VCF files never get annotated with PG tag for CalculateGenotypePosteriors
written by lait
-
How to add trio information to VCF or PED format (to compute Mendel error in Plink)
written by olavur
-
is it possible to Improve the Phasing of Family Trios using both GATK PhaseByTransmission and ReadB…
written by shajib.sust •
-
is it possible to Improve the Phasing of Family Trios using both GATK PhaseByTransmission and ReadB…
written by shajib.sust •
-
GATK CombineVCF How to order the genotypes/samples?
written by quachtina96 •
-
Phasing trios for identification of denovo variants
written by newbee •
-
Trio-based analysis: pipeline for phasing the data
written by newbee •
-
phasing de novo mutations
written by peter.krawitz •
-
1000 Genomes: Where To Get Samples Description
written by Chronos
Dear Jeremy Leipzig,
Thank you very much for your reply... I will be very happy to get some more suggestions from you. Is there anyway to phase all of the child genotypes using both the PhaseByTransmission and ReadBackedPhasing for a given family trio genotype information?
With Kind Regards,
-Ruhul
You can do
PhaseByTransmissionfirst, thenReadBackedPhasingwith the-respectPhaseInputoption, which will keep the PhaseByTransmission phases.Hi, GATK4 doesn' include PhaseByTransmission. So my question is how to do that. Thanks.