Picard FilterSamReads not working

Hello,

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.