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Picard FilterSamReads not working
I am using FilterSamReads in Picard to remove reads from a BAM file that are 1) marked as either both first/second of pair and 2) do not have a mate pair. I am supplying the program with a .txt file containing a list of the reads that I wish to exclude.
Unfortunately, when I run ValidateSamFile, the new BAM file from FilterSamReads still has all the reads I thought it had deleted.
Here is the command I'm using.
java -jar FilterSamReads.jar I=example.bam EXCLUDE_READS=reads_to_remove.txt O=GG_example_filtered.bam
Any help would be greatly appreciated.