MOPline v1.8.3.1

The codes in merge_SV_calls_multi_tools.pl, merge_SV_calls_ALLsamples.pl, and genotype_SV_SMC_7.4.pl were changed to give priority to INS lengths called in INSurVeyor.

MOPline-v1.8.3

(1) Adding a run_SVcallers_batch.pl script which enables batch runs of SV callers with multiple samples without using job management systems.
(2) Adding a run_create_cov_batch.pl script which enables batch runs of 'create_cov' with multiple samples without using job management systems.

MOPline-v1.8.2

(1) Scripts for creating gap bed and STR/SimpleRepeat files were added.
(2) The codes for run_CNVnator.pl, run_inGAP.pl, run_single.pl, run_batch_slurm.pl, run_batch_LSF.pl, run_single_singularity.pl, run_batch_slurm_singularity.pl, and run_batch_LSF_singularity.pl were fixed to fit a wide range of non-human species.
(3) Singularity definition file was corrected to decrease the file size of created sif file.
(4) A direct download method for the Singularity sif file was provided.
(5) A bug in scripts/run_SVcallers/run_MELT.pl was fixed: the melt_target default option for human (specified with -mt) was specified as 'ALU,LINE1,SVA,HERVK'.

MOPline-v1.8.1

Three presets (MOPline-8t, MOPline-7t-1, MOPline-7t-2) and the run_INSurVeyor.pl script have been added to allow the use of INS calls from INSurVeyor (Rajaby et al., Nat. Commun. 14, 3243 2023; https://github.com/kensung-lab/INSurVeyor). See README for details. However, we assume that you will run the tool using the singularity sif file provided on INSurVeyor's github site, so our singularity def file (mopline.def) does not include INSurVeyor's installation description.

MOPline-v1.8

(1) Enabled to automatically select the T2T-CHM13.v2.0 human reference data by specifying the --build option (-b T2T) in any scripts.
(2) Modified the code of genotype_SV_SMC_7.4.pl for SMC with changing the setting of flanking coverage of DEL and DUP.
(3) For >= 1 Kb DELs, the DPR calculated with all reads was used if the DPR was greater than 1.0.
(4) For human references, modified low confidence region files (Low_confidence.bed, Low_confidence.b38.bed, and Low_confidence.T2T-chm13.v2.0.bed) for filtering are provided.
(5) Singularity Definition file (mopline.def) for executing SV calling with multiple SV detection algorithms is provided.

MOPline-v1.7

The first release of MOPline package