The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
ReadBackedPhasing of trio with 3 bams
I have applied PhaseByTransmission on a trio with a ped file and now want to run ReadBackedPhasing. However, each of the trio variant calls were called from a different BAM file (as each was from a different individual). In the ReadBackedPhasing documentation it only mentions using the program with a single bam. Does this mean that I need to merge the bams for each of the three individuals into a single bam? If so, do you have any suggested programs that work well with GATK?