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while using PhaseByTransmission I always get this error:
INFO 23:07:16,945 PhaseByTransmission - Caution: Family F1 has 1 members; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.
This is the PED file:
F1 26779 31599 31600 2 2
F2 31599 0 0 2 0
F3 31600 0 0 1 0
And the command line:
java -Xmx2g -jar /home/common/GenomeAnalysisTK-2.1-13/GenomeAnalysisTK.jar \ -R /home/common/hg19/ucschg19/ucsc.hg19.fasta \ -T PhaseByTransmission \ -V 38Ind_batch01_ped_snps.raw.SNP.filtered.vcf \ -ped familys.ped \ -pedValidationType SILENT \ -o 38Ind_batch01_ped_snps.raw.SNP.filtered.phasedBT.vcf
PhaseByTransmission then only rewrites the VCF file without any phasing done. Is there something wrong with the commandline or is the PED file malformated?