Pileup output of GATK4 vs. GATK3Answered
I am updating our workflow from GATK3.x to GATK4.x. The current protocol depends on the refined bam files generated ("This app outputs the refined (deduplicated, realigned, and recalibrated) mappings in BAM format (*.bam), as well as the associated BAM index (*.bai).") to obtain pileup files for coverage analysis. Therefore I am wondering, if I use the setting below will GATK4 refine the input bam file and use it to generate the pileup file. Do GATK4 vs. GATK3 have similar performance in this case? Thanks.
gatk Pileup \ -R reference.fasta \ -I input.bam \ -O output.txt
Hi Ran Wei,
We looked through the GATK Pileup code and confirmed that the results should be mostly the same comparing GATK3 and GATK4. There are very small differences with how GATK3 and GATK4 work internally so you might see very minor differences. However, the GATK4 version was built with GATK3 compatibility in mind so you shouldn't have any issues.
Please let me know if you have any issues or further questions.
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