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Wrong genotype correction for hemizygote after PhaseByTransmission
I have a WEX data set for a trio and I followed the best practices for variant calling. PhaseByTransmission updated some genotypes, including one we already validated by sanger.
See attachments for the variants and the PED. First variant in the file is after phasing. The affected male is in the last column, his parents are the preceding 2. The variant gets updated from 1/1 to 1|0 but since it is chrX and the affected individual is male I would expect this never to happen.
The command I used:
java -Xmx4g -jar GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -R hg19.fa -T PhaseByTransmission \
-V UG8.filtered.SNP.InDel.vcf \
-ped /home/corona/Desktop/pedfiles/VUSerie1.ped \
-o UG8.phased.filtered.SNP.InDel.vcf \
I had to use -pedValidationType SILENT because I had a family in my VCF that was not in my ped. I extracted the samples from the vcf and tried again with STRICT validation and got the same results.