I can't find a guidline for which of the two gathered .bam files to use for mobile element discovery. Here is an example code:

java -Xmx4G -jar MELT.jar Genotype -p ALU -w ALU -bamfile ALU/INDIVIDUAL1.md.chrFilter.ALU.aligned.pulled.sorted.bam -h ${refFasta} -t $meltProg/me_refs/Hg38/ALU_MELT.zip -d 10000

The file "INDIVIDUAL1.md.chrFilter.ALU.aligned.pulled.sorted.bam" has an alternative called "INDIVIDUAL1.md.chrFilter.ALU.aligned.final.sorted.bam". Although "final" one crashes, the "pulled" bam also produces subpar results so i'm confused. If you have done the analysis, could you advise the proper way to do it?