Question: How does GATK PhaseByTransmission define the phasing of Father and Mother?
3
gravatar for shajib.sust
3.4 years ago by
shajib.sust40
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,
-Ruhul

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by shajib.sust40

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

ADD REPLYlink written 7 weeks ago by mcclintock10
2
gravatar for Jeremy Leipzig
3.4 years ago by
Philadelphia, PA
Jeremy Leipzig18k 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 3.4 years ago by Jeremy Leipzig18k
0
gravatar for shajib.sust
3.4 years ago by
shajib.sust40
United States
shajib.sust40 wrote:

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 

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by shajib.sust40

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

ADD REPLYlink written 3.2 years ago by ebrown1955290
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