Madeline Couse

Hi Brian, Thanks for replying. No, I don't expect LoF_flags to always have a value, but we have tested a number of variants that are present in gnomAD that do...

[hpcuser01@friedmanhpc03:/]> python /usr/local/bin/run_metasv.py --reference mnt/data/GRCh37_bcgsc/GRCh37-lite.fa --breakdancer_native home/hpcuser01/breakdancer/perl/A10898_breakdancer --breakseq_native home/hpcuser01/work/breakseq.gff --cnvnator_native home/hpcuser01/CNVnator_v0.3.2/src/A10898_100_cnvnator --pindel_native home/hpcuser01/pindel-master/A10898_D home/hpcuser01/pindel-master/A10898_LI home/hpcuser01/pindel-master/A10898_SI home/hpcuser01/pindel-master/A10898_TD home/hpcuser01/pindel-master/A10898_INV --sample A10898 --bam mnt/data/A10898_3_lanes_dupsFlagged.bam --spades home/hpcuser01/SPAdes-3.6.2-Linux/bin/spades.py --age home/hpcuser01/AGE-simple-parseable-output/age_align --num_threads 15 --workdir mnt/data/A10898_work --outdir...

I tried the above with 2 threads, and eventually got these error messages: INFO 2016-03-22 07:07:43,216 run_age_single- Returned code 0 (0.129607 seconds) ERROR 2016-03-22 07:07:43,233 run_age_single- Caught exception in worker...

I will try out 0.5.4. I used Lumpy and CNVnator previously, as well, without assembly.

I'm having the same issue with the latest release. When the --boost_scs option is used to enhance insertion sensitivity detection, it interferes with DEL detection, decreasing the sensitivity from 80%...

[metaSV_output.txt.gz](https://github.com/bioinform/metasv/files/718206/metaSV_output.txt.gz) The mean coverage was 30X

@marghoob Have you identified the issue?

I expect about 800 high-confidence deletions and a varSim sensitivity of 80%. This is the output when the --boost_scs option is not used. With --boost_scs, I get 99 high confidence...

Here's the vcf: [metaSV_boostsc.vcf.gz](https://github.com/bioinform/metasv/files/751475/metaSV_boostsc.vcf.gz)

All the bed files including those in the numbered subfolders within the work directory?