I'm using GATK to analyze some paired-end Illumina exome data and have been running into a problem after realignment using IndelRealigner. After realignment, I have been trying to use Picard's FixMateInformation to take the realigned query-name-sorted bams and produce fixed, coordinate-sorted bams. This function creates a bunch of temp files and does so fairly quickly. However, the process of merging these temp files together takes an extraordinarily long time. Not sure what I'm doing wrong here.
Is it possible to simply use the FixMate and Sort functions in SamTools to perform the same task? This I've done and it works relatively quickly.
Lastly, one other quick question, after realignment using IndelRealigner, a one exome bam file which is only about 7.3 GB (following initial alignment with BWA) becomes approximately 32.8 GB. Is this supposed to happen?
Thanks, Toast
Is it possible to simply use the FixMate and Sort functions in SamTools to perform the same task? This I've done and it works relatively quickly.
Lastly, one other quick question, after realignment using IndelRealigner, a one exome bam file which is only about 7.3 GB (following initial alignment with BWA) becomes approximately 32.8 GB. Is this supposed to happen?
Thanks, Toast
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