I am currently focusing on identifying denovo mutations from my trio data (parents are unaffected and child is affected). I used PhaseByTransmission. However, I found all denovo mutations (child is heterozygous, and both parents are hom. ref) were not phased (i.e. I am getting '/' instead of '|'). Do you think it is an error? If I search autosomal recessive, variants were phased correctly. What is the problem in my analysis? I am pasting the summary results provided by PhaseByTransmission for your kind perusal. Please also comment on the summary results, are they looking odd?
java -jar /gatk_3.3/GenomeAnalysisTK.jar -R /reference_sequence/human_g1k_v37.fasta -T PhaseByTransmission -V trio1.vcf -ped trio1.ped --DeNovoPrior 0.00001 -o trio_out.vcf --MendelianViolationsFile mendelian_violation.vcf INFO 20:04:04,201 GenomeAnalysisEngine - Strictness is SILENT INFO 20:04:04,341 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 20:04:04,453 PedReader - Reading PED file trio1.ped with missing fields:  INFO 20:04:04,457 PedReader - Phenotype is other? false INFO 20:04:04,510 GenomeAnalysisEngine - Preparing for traversal INFO 20:04:04,530 GenomeAnalysisEngine - Done preparing for traversal INFO 20:04:04,531 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 20:04:04,531 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 20:04:04,532 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 20:04:34,824 ProgressMeter - 15:96876611 147844.0 30.0 s 3.4 m 77.5% 38.0 s 8.0 s INFO 20:04:43,701 PhaseByTransmission - Number of complete trio-genotypes: 139299 INFO 20:04:43,702 PhaseByTransmission - Number of trio-genotypes containing no call(s): 0 INFO 20:04:43,703 PhaseByTransmission - Number of trio-genotypes phased: 124651 INFO 20:04:43,703 PhaseByTransmission - Number of resulting Het/Het/Het trios: 13391 INFO 20:04:43,704 PhaseByTransmission - Number of remaining single mendelian violations in trios: 937 INFO 20:04:43,704 PhaseByTransmission - Number of remaining double mendelian violations in trios: 12 INFO 20:04:43,704 PhaseByTransmission - Number of complete pair-genotypes: 0 INFO 20:04:43,705 PhaseByTransmission - Number of pair-genotypes containing no call(s): 0 INFO 20:04:43,705 PhaseByTransmission - Number of pair-genotypes phased: 0 INFO 20:04:43,705 PhaseByTransmission - Number of resulting Het/Het pairs: 0 INFO 20:04:43,706 PhaseByTransmission - Number of remaining mendelian violations in pairs: 0 INFO 20:04:43,706 PhaseByTransmission - Number of genotypes updated: 4395 INFO 20:04:45,481 ProgressMeter - done 201351.0 40.0 s 3.4 m 100.0% 40.0 s 0.0 s INFO 20:04:45,482 ProgressMeter - Total runtime 40.95 secs, 0.68 min, 0.01 hours INFO 20:04:47,002 GATKRunReport - Uploaded run statistics report to AWS S3