Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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 \
PhaseByTransmission then only rewrites the VCF file without any phasing done.
Is there something wrong with the commandline or is the PED file malformated?