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Hi, I'm trying to find mutations in Illumina exome sequence using GATK. I'm doing one chr at a time. I have managed to get to a vcf for chr1 that has been PhasedByTransmission but am a bit unsure about how to get the next phasing done.
Specifically ReadBackedPhasing. I'm aware I need to tell it to respect the Transmission phasing but have two questions that are holding me back.
1) My vcf was generated with my Trio alongside about 30 other exomes. Do I need to tell the ReadBackedPhasing to ignore these others/only phase my trio of samples?
2) It says to provide a .bam. Which ones? Just the ones for my Trio with seperate -I entries eg -I sample1.bam -I sample2.bam -i sample3.bam etc or -I sample1.bam samples2.bam sample3.bam OR do I just do one sample at a time (presumably not since I'd end up with three different vcfs wouldn't I?!
Any help appreciated.
FGPonce
Specifically ReadBackedPhasing. I'm aware I need to tell it to respect the Transmission phasing but have two questions that are holding me back.
1) My vcf was generated with my Trio alongside about 30 other exomes. Do I need to tell the ReadBackedPhasing to ignore these others/only phase my trio of samples?
2) It says to provide a .bam. Which ones? Just the ones for my Trio with seperate -I entries eg -I sample1.bam -I sample2.bam -i sample3.bam etc or -I sample1.bam samples2.bam sample3.bam OR do I just do one sample at a time (presumably not since I'd end up with three different vcfs wouldn't I?!
Any help appreciated.
FGPonce