I tried running ValidateSamFile on a bam file (to troubleshoot a different problem), but got an error message stating that "ValidateSamFile Value was put into PairInfoMap more than once"
This bam file was prepared from a PCR-free library, so there should not be duplicated reads. However, I did merge two separate sorted bam files in order to create this final bam file, called Ancestors.final.bam, that I ran ValidateSamFile on.
Is the issue that I have merged two technical replicates, causing some rads to have the same values? How can I overcome this problem and still merge the technical replicate bam files?
Thanks for your help! My GATK version, code, and output messages are pasted below.
GATK version used: 18.104.22.168
Picard version used: 2.14.0
Exact command used: java -jar ~/libraries/picard/picard.jar ValidateSamFile I=Ancestors.final.bam MODE=SUMMARY
Entire error log:
ERROR 2021-02-12 15:12:09 ValidateSamFile Value was put into PairInfoMap more than once. 1: A00975:57:HHGM7DRXX:2:1131:23936:21214
[Fri Feb 12 15:12:09 EST 2021] picard.sam.ValidateSamFile done. Elapsed time: 2.88 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
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