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?
Did you find the answer for this? I have the same doubt.