Deletion assembly and soft clip

[Madelinehazel]

Hello,

There seems to be some bug in metaSV when the --boost_scs option is included. With this option, my deletion detection sensitivity drops dramatically from ~80% to 5% (as measured using VarSim). My command is as follows, using metaSV v 0.5.3: run_metasv.py --bam $BAM \ --reference $REF \ --sample $SAMPLE --boost_sc \ --cnvnator_native $SAMPLE.bam_CNVcall.100 \ --lumpy_vcf $SAMPLE.bam_lumpy.vcf \ --spades /home/hpcuser01/SPAdes-3.6.2-Linux/bin/spades.py \ --age /home/hpcuser01/AGE/age_align \ --min_support_ins 2 \ --max_ins_intervals 500000 --isize_mean $INSMEAN --isize_sd $INSSD \ --num_threads $THREADS --outdir $SAMPLE.metaSV.out --workdir $SAMPLE.metaSV.work Even if I specify --svs_to_assembly INS I still have deletions dropping out. Not sure why this is.