I am trying to use ADTEx on my exome sequencing data following the user guide instructions. The problem is that despite the fact I am not getting any error during running the command, the calculated coverage files for sample and normal bam files are endless;what I mean is that ADTEx keeps writing coverage file like forever and the coverage files are a lot of GBs (>700) and eventually my server crashes due to lack of free space. I also tried to obtain the depth of coverage using bedtools but I am still facing the same problem. What I suspect is that ADTEx and bedtools don t use my target bed file to calculate the specific regions coverage. Any ideas what s happening? My target.bed seems normal and I successfully used it in other software (chromosome names are same both in bam and target). Please see the ADTEx and bedtools commands below.
python ADTEx.py --normal ~/Desktop/processed_reads/mouse_3/m3_Liver_processed_realigned.bam --tumor ~/Desktop/processed_reads/mouse_3/m3_T1Bm1_processed_realigned.bam --bed ~/Desktop/mm10_bed_files/mm10_targets.bed --ploidy 2 --plot --minReadDepth 50 --out ~/Desktop/m3T1Bm1 coverageBed -abam ~/Desktop/processed_reads/mouse__T1Bm1_processed_realigned.bam -b ~/Desktop/mm10_bed_files/mm10_targets.bed -d > ~/Desktop/coverage.txt
Thank you in advance!