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Error message during PhaseByTransition
Hi, I am running PhaseByTransition on a set of 250+ family trios. I am getting this error message:
Sample lgsnd32563jz3 found in data sources but not in pedigree files with STRICT pedigree validation
However, the sample is in the pedigree file. I tried adding the flag recommended in previous forums - --pedigreeValidationType SILENT, but then all the trios were excluded.
Can you advise me on what the problem could be? Here is my command:
java -Xmx8g -jar GenomeAnalysisTK.jar -T PhaseByTransmission -R /Volumes/Thunderbolt/ref_genome/human_g1k_v37.fasta -V /Volumes/Passport2/July2016/merged_vcf/Trios_GATK_all.dbID.db.eff.vcf -ped /Users/Yam/Desktop/Trios.ped -o /Volumes/Passport2/July2016/merged_vcf/Trios_GATK_all.dbID.db.eff_phased.vcf