Expected deletion in mock sample not being called

[zhemingfan]

Hi @friend1ws,

System Info

System Information	Version
OS	Ubuntu 18.04.2 LTS
python	3.8.3
singularity	3.5.2-1.1.el7
nanomonsv	nanomonsv_0.5.0--pyhdfd78af_0.sif

Expected Behaviour:

We expect that a deletion at chr14: 104093749-104093805 is found in a mock sample output: SAMPLE.nanomonsv.result.txtand COLO829.nanomonsv.result.vcf.

Tumour (further reads are excluded) - from SAMPLE.deletion.sorted.bed.gz:

chr14   104093740       104093789       de6f0954-58ea-40d4-af58-a522b3cfc650    49      +       23,21303,64422,64438,-,60,63125,1275,1669,False,False
chr14   104093748       104093805       a0a18aac-9e3c-43fd-bf5c-ce5a3441fa73    57      +       24,32792,53268,53269,+,60,52626,619,617,False,False
chr14   104093749       104093805       0827b9da-7477-46d1-9efc-bca715f734dd    56      +       24,9978,17224,17240,+,60,16819,382,182,False,False
chr14   104093749       104093805       11573b32-f300-44f9-bcdb-47d94e33f05e    56      +       8206,15517,19900,19915,+,60,11561,134,245,False,False
chr14   104093749       104093805       26149c33-f8a9-4c19-8ac4-ea501c517f27    56      +       21,10880,25633,25648,+,60,25175,438,328,False,False
chr14   104093749       104093805       2db02a22-8383-46c1-8d50-09a6e25edf82    56      +       25,831,3948,3964,+,60,3886,38,73,False,False
chr14   104093749       104093805       317f9492-de2b-46f2-8b03-d36d2192522c    56      +       18,21928,25832,25842,+,60,25323,492,324,False,False
chr14   104093749       104093805       3635ef88-90a4-4fe1-9e25-277d11d08040    56      +       29,6222,9897,19774,-,60,9680,189,234,True,False
chr14   104093749       104093805       368ff285-6455-4dec-a16b-6afc16f175c2    56      +       18,20056,23721,23736,-,60,23334,370,522,False,False
chr14   104097882       104097922       6734c5a6-08dd-4a55-94b2-7c1f047837ec    40      +       24,12922,17821,17836,+,60,17404,394,848,False,False

Nearest Control - from SAMPLE.deletion.sorted.bed.gz:

chr14   104085984       104086089       d092b848-989a-41fe-af70-d3e6ecf37b42    105     +       456,898,9178,9193,-,60,8479,244,375,False,False
chr14   104094705       104094741       81a9d378-04fa-4c02-b0c7-0af9d4f9fa7b    36      +       25,12934,17643,17660,-,60,17441,178,461,False,False
chr14   104098021       104098053       9cb4bc4b-5132-469b-9185-77dadd0cde84    32      +       24,10660,11984,24165,-,60,11801,160,219,True,False

Nearest Known SVs:

chr14   104093673       104093708       *       35      +       1       HG03453_25
chr14   104093767       104093808       *       41      +       1       HG01175_8
chr14   104093770       104093803       *       33      +       1       HG03540_28
chr14   104093817       104093963       *       146     +       1       HG02257_17

Commands Ran:

singularity exec -B /projects,/home /path/to/nanomonsv_0.5.0--pyhdfd78af_0.sif nanomonsv parse /path/to/BAM/SAMPLE.bam SAMPLE

singularity exec -B /projects,/home /path/to/nanomonsv_0.5.0--pyhdfd78af_0.sif \
  nanomonsv \
    get \
    /tumour_folder/SAMPLE \
    /path/to/tumour.bam \
    /reference/hg38_no_alt.fa \
    --control_prefix /path_to/SAMPLE \
    --control_bam /path_to/CONTROL.bam \
    --processes 72 \
    --single_bnd \
    --use_racon \
    --control_panel_prefix /nanomonsv/hprc_year1_data_freeze_nanopore_minimap2_2_24_merge_control/hprc_year1_data_freeze_nanopore_minimap2_2_24_merge_control

Question:

Could you possibly suggest some reasons why this SV isn't being called?

[zhemingfan]

Closing as newer version seems to resolve this.