Problem with Jitterbug filtering

[brguez]

Dear developers,

We are testing Jitterbug in a deeply sequenced sample (300x). Apparently the execution was ok as all the output files were generated. However, most of the insertions are lost in the filtering step (only 53/90295 pass the filtering).

Do you have any clue why this is happening? we would expect ~1200 germline MEI in this sample.

Here are the commands we've used:

jitterbug.py --numCPUs 10 --mem --output_prefix "$output_dir"/"$sample_name" "$sample_bam" ./data/hg19.te_annots.gff

jitterbug_filter_results_func.py -g "$output_dir"/"$sample_name".TE_insertions_paired_clusters.gff3 -c "$output_dir"/"$sample_name".filter_config.txt -o "$output_dir"/"$sample_name".TE_insertions_paired_clusters.filtered.gff3

This is the log for the filtering step:
Total rows = 90295
Passed rows =53

Description of the non passed rows:
Problems with softclip support: 87780
Wrong interval size: 25129
Wrong span size: 11744
Inconsistency of TE family FWD and REV: 1242
Wrong cluster size: 0

Thanks!
Berni

[CPTPaso]

Same problem on my end. Could you somehow solve this issue?