I'm having a problem calling SNPs from a sorted bam file with GATK HaplotypeCaller. The file is a merged file of two technical replicates that were each sequenced on different lanes and aligned to the reference genome. When I run Picard ValidateSamFile on the bam file, I got the following error: "ValidateSamFile Value was put into PairInfoMap more than once." I also ran ValidateSamFile on the intermediate sam file for this sample (before its was converted to bam and sorted), and ValidateSamFile did not give me that error message when ran on the sam file. So, it appears that during the step where the sam file was converted into a bam file and sorted with samtools sort, something about read group information was disrupted.
Has anyone encountered this before, or have an ideas as to what would cause this issue? I tried aligning this sample to the reference genome again using the -M tag in bwa-mem (initially I didn't use the -M tag), but this issue wasn't resolved. I haven't been able to find much information about this error, other than suggestions to run Picard AddOrReplaceReadGroups to rename read group information. I'm will likely try this next but I'm going to need to call SNPs on a handful of files like this, so if possible I'd to figure out and fix what the underlying problem is before I resort to replacing the read group information for each sample.
Thank you in advance for your help!