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Exception in MarkDuplicates Value was put into PairInfoMap more than once
I am relatively new to GATK and stuck on this problem.
After downloading the bam file that I wish to analyze, I am cutting portions of the file because I only wish to analyze variants at specific genes. Once I have the smaller files for each gene, I am using samtools merge to merge all of the smaller files back into one full sliced bam file. Next, I am realigning this file using bwa aln and sampe. After this step, I am attempting to use GATK best practices to mark the variants in these genes.
First, I am using GATK AddOrReplaceReadGroups to modify read group information as necessary. Then, I am using Picard's MarkDuplicates to mark duplicates in the re-aligned bam file. However, I get the following error.
Exception in thread "main" net.sf.picard.PicardException: Value was put into PairInfoMap more than once. 156: TLL:HWI-ST1222:5:2308:12532:76745#0 at net.sf.picard.sam.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:124) at net.sf.picard.sam.CoordinateSortedPairInfoMap.remove(CoordinateSortedPairInfoMap.java:78) at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:61) at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:418) at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:161) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:145)
Looking at Picard's FAQ page (https://broadinstitute.github.io/picard/faq.html), it suggests that I try using Picard's MergeBamAlignment which also fails giving an error suggesting that the error is in the record ID of the bam file.
Exception in thread "main" net.sf.picard.PicardException: Program Record ID already in use in unmapped BAM file. at net.sf.picard.sam.SamAlignmentMerger.<init>(SamAlignmentMerger.java:131) at net.sf.picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:226) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.sam.MergeBamAlignment.main(MergeBamAlignment.java:205)
Continuing on, trying to change the options on samtools merge to change the record ID's when merging together the single files into the full sliced file also failed.
Some more work into these issues found that using samtools fixmate and then Picard SortSam before calling MarkDuplicates resolves the issue, but the total amount of variants called by GATK is different when I run the sliced file through against a single gene file (for the same locations).
Are there any other options to explore to resolve this error?