Question: How does GATK PhaseByTransmission define the phasing of Father and Mother?
gravatar for shajib.sust
5.3 years ago by
United States
shajib.sust40 wrote:

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,

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by shajib.sust40

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,

ADD REPLYlink modified 15 months ago by Ram32k • written 5.3 years ago by shajib.sust40

You can do PhaseByTransmission first, then ReadBackedPhasing with the -respectPhaseInput option, which will keep the PhaseByTransmission phases.

ADD REPLYlink modified 15 months ago by Ram32k • written 5.1 years ago by ebrown1955300

Hi, GATK4 doesn' include PhaseByTransmission. So my question is how to do that. Thanks.

ADD REPLYlink written 2.1 years ago by mcclintock10
gravatar for Jeremy Leipzig
5.3 years ago by
Philadelphia, PA
Jeremy Leipzig19k wrote:

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.

ADD COMMENTlink written 5.3 years ago by Jeremy Leipzig19k
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