False positives CNV called for chrX in men

[Tintest]

Hello,

I did the CNV call one by one on my cohort of 26 samples. Of all the CNVs called, 253 out of 254 were on the X chromosome. All of these CNVs were called in males (although the cohort is almost equally made up of males and females).

However, I think I've used the --ploidy-chr parameter correctly, see exemple command below.

singularity exec --bind /srv:/srv spectre.0.2.0.sif spectre CNVCaller \
  --coverage mosdepth/Sample1.regions.bed.gz mosdepth/Sample2.regions.bed.gz mosdepth/Sample3.regions.bed.gz mosdepth/Sample4.regions.bed.gz mosdepth/Sample5.regions.bed.gz mosdepth/Sample6.regions.bed.gz mosdepth/Sample7.regions.bed.gz mosdepth/Sample8.regions.bed.gz mosdepth/Sample9.regions.bed.gz mosdepth/Sample10.regions.bed.gz mosdepth/Sample11.regions.bed.gz mosdepth/Sample12.regions.bed.gz mosdepth/Sample13.regions.bed.gz mosdepth/Sample14.regions.bed.gz mosdepth/Sample15.regions.bed.gz mosdepth/Sample16.regions.bed.gz mosdepth/Sample17.regions.bed.gz mosdepth/Sample18.regions.bed.gz mosdepth/Sample19.regions.bed.gz mosdepth/Sample20.regions.bed.gz mosdepth/Sample21.regions.bed.gz mosdepth/Sample22.regions.bed.gz mosdepth/Sample23.regions.bed.gz mosdepth/Sample24.regions.bed.gz mosdepth/Sample25.regions.bed.gz mosdepth/Sample26.regions.bed.gz  \
  --sample-id Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9 Sample10 Sample11 Sample12 Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 Sample19 Sample20 Sample21 Sample22 Sample23 Sample24 Sample25 Sample26 \
  --output-dir results/Sample1/ \
  --blacklist grch38_blacklist_spectre.bed \
  --only-chr chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY \
  -0 \
  --ploidy-chr chrX:1,chrY:1 \
  --reference GRCh38.p13.canonical.fa.gz 

Most of the CNVs called are deletions and have recurrent coordinates.

Here is the CNV called by Spectre :

  Sample4 chrX    4002000 END=8605000;SVLEN=4603000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE       0/1:0:0:0.51
Sample25        chrX    4002000 END=31062000;SVLEN=27060000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample17        chrX    4002000 END=31075000;SVLEN=27073000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample21        chrX    4002000 END=31075000;SVLEN=27073000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample10        chrX    4002000 END=31075000;SVLEN=27073000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample23        chrX    4002000 END=31075000;SVLEN=27073000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample24        chrX    4002000 END=31080000;SVLEN=27078000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.51
Sample19        chrX    4002000 END=31085000;SVLEN=27083000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample12        chrX    4002000 END=31110000;SVLEN=27108000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample5 chrX    4002000 END=31130000;SVLEN=27128000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample16        chrX    4002000 END=31474000;SVLEN=27472000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.53
Sample13        chrX    4002000 END=31851000;SVLEN=27849000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.53
Sample8 chrX    4002000 END=36999000;SVLEN=32997000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.53
Sample14        chrX    4002000 END=36999000;SVLEN=32997000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample15        chrX    4002000 END=36999000;SVLEN=32997000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample4 chrX    8638000 END=31092000;SVLEN=22454000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample16        chrX    31069000        END=33362000;SVLEN=2293000;SVTYPE=DUP;CN=4;SVSUPPORT=FALSE      1/1:0:0:4.02
Sample10        chrX    31083000        END=36999000;SVLEN=5916000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.63
Sample17        chrX    31089000        END=36999000;SVLEN=5910000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.62
Sample13        chrX    31862000        END=33353000;SVLEN=1491000;SVTYPE=DUP;CN=5;SVSUPPORT=FALSE      ./.:0:0:4.65
Sample19        chrX    33331000        END=36999000;SVLEN=3668000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample12        chrX    33342000        END=36999000;SVLEN=3657000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.49
Sample23        chrX    33342000        END=36999000;SVLEN=3657000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample4 chrX    33354000        END=36999000;SVLEN=3645000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.53
Sample25        chrX    33359000        END=36999000;SVLEN=3640000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.52
Sample16        chrX    33359000        END=36999000;SVLEN=3640000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.54
Sample13        chrX    33362000        END=36999000;SVLEN=3637000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.49
Sample5 chrX    33362000        END=36999000;SVLEN=3637000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample24        chrX    33363000        END=36999000;SVLEN=3636000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.53
Sample21        chrX    33365000        END=36999000;SVLEN=3634000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample23        chrX    38001000        END=40030000;SVLEN=2029000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample4 chrX    38001000        END=40030000;SVLEN=2029000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.48
Sample5 chrX    38001000        END=40035000;SVLEN=2034000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample12        chrX    38001000        END=40040000;SVLEN=2039000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample21        chrX    38001000        END=40061000;SVLEN=2060000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample19        chrX    38001000        END=40110000;SVLEN=2109000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample24        chrX    38001000        END=40114000;SVLEN=2113000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.48
Sample8 chrX    38401000        END=40026000;SVLEN=1625000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.49
Sample25        chrX    38401000        END=40046000;SVLEN=1645000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample17        chrX    38425000        END=40060000;SVLEN=1635000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample10        chrX    38443000        END=40023000;SVLEN=1580000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample16        chrX    38445000        END=40025000;SVLEN=1580000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.54
Sample14        chrX    38445000        END=40030000;SVLEN=1585000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample15        chrX    38446000        END=40026000;SVLEN=1580000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample13        chrX    38450000        END=40019000;SVLEN=1569000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.47
Sample25        chrX    40154000        END=48619000;SVLEN=8465000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.52
Sample12        chrX    40169000        END=49199000;SVLEN=9030000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample23        chrX    40178000        END=48766000;SVLEN=8588000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample17        chrX    40179000        END=48684000;SVLEN=8505000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample10        chrX    40192000        END=48517000;SVLEN=8325000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample15        chrX    40194000        END=48759000;SVLEN=8565000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample19        chrX    40196000        END=48766000;SVLEN=8570000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample16        chrX    40198000        END=48249000;SVLEN=8051000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.53
Sample14        chrX    40198000        END=48593000;SVLEN=8395000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample5 chrX    40199000        END=48766000;SVLEN=8567000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample24        chrX    40199000        END=48771000;SVLEN=8572000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample13        chrX    40200000        END=48760000;SVLEN=8560000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.47
Sample4 chrX    40201000        END=48760000;SVLEN=8559000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample8 chrX    40201000        END=48786000;SVLEN=8585000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample21        chrX    40202000        END=48782000;SVLEN=8580000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample10        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample17        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample19        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample21        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample24        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample13        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.48
Sample15        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.49
Sample12        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample23        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample4 chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample8 chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample14        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample16        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample25        chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample5 chrX    50401000        END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample10        chrX    53001000        END=55399000;SVLEN=2398000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample5 chrX    53001000        END=55399000;SVLEN=2398000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample19        chrX    53001000        END=55399000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample23        chrX    53001000        END=55399000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample8 chrX    53001000        END=55603000;SVLEN=2602000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample13        chrX    53001000        END=55607000;SVLEN=2606000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.46
Sample16        chrX    53001000        END=55617000;SVLEN=2616000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.52
Sample24        chrX    53001000        END=55627000;SVLEN=2626000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.49
Sample15        chrX    53001000        END=55632000;SVLEN=2631000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.49
Sample25        chrX    53001000        END=55659000;SVLEN=2658000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample4 chrX    53001000        END=55692000;SVLEN=2691000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.49
Sample12        chrX    53001000        END=55772000;SVLEN=2771000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.5
Sample17        chrX    53001000        END=55812000;SVLEN=2811000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample14        chrX    53001000        END=55852000;SVLEN=2851000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample21        chrX    53001000        END=57999000;SVLEN=4998000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample8 chrX    55076000        END=57999000;SVLEN=2923000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.52
Sample16        chrX    55092000        END=57999000;SVLEN=2907000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.54
Sample14        chrX    55097000        END=57999000;SVLEN=2902000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample15        chrX    55227000        END=57999000;SVLEN=2772000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample19        chrX    55242000        END=57999000;SVLEN=2757000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample4 chrX    55252000        END=57999000;SVLEN=2747000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.53
Sample5 chrX    55312000        END=57999000;SVLEN=2687000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample13        chrX    55389000        END=57999000;SVLEN=2610000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.48
Sample12        chrX    55601000        END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample17        chrX    55601000        END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample10        chrX    55601000        END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample23        chrX    55601000        END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample24        chrX    55601000        END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.52
Sample25        chrX    55611000        END=57992000;SVLEN=2381000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample21        chrX    63501000        END=71499000;SVLEN=7998000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample16        chrX    63501000        END=71499000;SVLEN=7998000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.53
Sample17        chrX    63501000        END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample14        chrX    63501000        END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample19        chrX    63501000        END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample24        chrX    63501000        END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample25        chrX    63501000        END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample5 chrX    63501000        END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample8 chrX    63501000        END=73022000;SVLEN=9521000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.52
Sample13        chrX    63501000        END=73057000;SVLEN=9556000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.47
Sample23        chrX    63501000        END=73057000;SVLEN=9556000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample10        chrX    63501000        END=73077000;SVLEN=9576000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample12        chrX    63501000        END=73082000;SVLEN=9581000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.5
Sample4 chrX    63501000        END=73082000;SVLEN=9581000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample15        chrX    63501000        END=73257000;SVLEN=9756000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE      0/1:0:0:0.51
Sample4 chrX    70280000        END=101367000;SVLEN=31087000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.53
Sample15        chrX    70610000        END=101375000;SVLEN=30765000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample17        chrX    71250000        END=123865000;SVLEN=52615000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.5
Sample16        chrX    71290000        END=101375000;SVLEN=30085000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.52
Sample24        chrX    71350000        END=101370000;SVLEN=30020000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.52
Sample25        chrX    71356000        END=101376000;SVLEN=30020000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.51
Sample8 chrX    71399000        END=101419000;SVLEN=30020000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.53
Sample14        chrX    71410000        END=101370000;SVLEN=29960000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample21        chrX    71415000        END=101369000;SVLEN=29954000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.5
Sample23        chrX    71419000        END=101389000;SVLEN=29970000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample5 chrX    71419000        END=101399000;SVLEN=29980000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.5
Sample19        chrX    71420000        END=101375000;SVLEN=29955000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample13        chrX    71465000        END=80570000;SVLEN=9105000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE      1/1:0:0:0.48
Sample10        chrX    71466000        END=101371000;SVLEN=29905000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.5
Sample12        chrX    71494000        END=101424000;SVLEN=29930000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.49
Sample13        chrX    80559000        END=101359000;SVLEN=20800000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.5
Sample15        chrX    101432000       END=114199000;SVLEN=12767000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.5
Sample14        chrX    101552000       END=116767000;SVLEN=15215000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.51
Sample10        chrX    101702000       END=114199000;SVLEN=12497000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.5
Sample19        chrX    101832000       END=114199000;SVLEN=12367000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample12        chrX    101847000       END=114199000;SVLEN=12352000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.5
Sample8 chrX    102057000       END=116812000;SVLEN=14755000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.52
Sample16        chrX    102067000       END=116717000;SVLEN=14650000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.53
Sample21        chrX    102087000       END=114199000;SVLEN=12112000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.5
Sample25        chrX    102128000       END=108843000;SVLEN=6715000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.51
Sample23        chrX    102167000       END=116752000;SVLEN=14585000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.5
Sample13        chrX    102168000       END=116753000;SVLEN=14585000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.48
Sample5 chrX    102172000       END=116707000;SVLEN=14535000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample4 chrX    102182000       END=116722000;SVLEN=14540000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample24        chrX    102192000       END=114199000;SVLEN=12007000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample25        chrX    108296000       END=114192000;SVLEN=5896000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.51
Sample23        chrX    116701000       END=120849000;SVLEN=4148000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample12        chrX    116701000       END=120849000;SVLEN=4148000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample21        chrX    116701000       END=120849000;SVLEN=4148000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample8 chrX    116701000       END=120849000;SVLEN=4148000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample24        chrX    116701000       END=121119000;SVLEN=4418000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample19        chrX    116701000       END=121129000;SVLEN=4428000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample16        chrX    116701000       END=121134000;SVLEN=4433000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.53
Sample14        chrX    116701000       END=121154000;SVLEN=4453000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.51
Sample15        chrX    116701000       END=121174000;SVLEN=4473000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample4 chrX    116701000       END=121234000;SVLEN=4533000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample10        chrX    116701000       END=121299000;SVLEN=4598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample5 chrX    116701000       END=121314000;SVLEN=4613000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample13        chrX    116711000       END=121267000;SVLEN=4556000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.47
Sample25        chrX    116711000       END=121647000;SVLEN=4936000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample14        chrX    120699000       END=123844000;SVLEN=3145000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample5 chrX    120708000       END=123843000;SVLEN=3135000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample21        chrX    120713000       END=123835000;SVLEN=3122000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample13        chrX    120771000       END=123836000;SVLEN=3065000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample24        chrX    120793000       END=123848000;SVLEN=3055000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample25        chrX    120799000       END=123864000;SVLEN=3065000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.52
Sample10        chrX    120814000       END=123864000;SVLEN=3050000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample16        chrX    120844000       END=123904000;SVLEN=3060000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.54
Sample8 chrX    120848000       END=123879000;SVLEN=3031000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample15        chrX    121101000       END=123834000;SVLEN=2733000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample19        chrX    121101000       END=123834000;SVLEN=2733000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample23        chrX    121101000       END=123839000;SVLEN=2738000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample12        chrX    121101000       END=123864000;SVLEN=2763000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample4 chrX    121101000       END=123894000;SVLEN=2793000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample19        chrX    124400000       END=129965000;SVLEN=5565000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample10        chrX    124425000       END=129954000;SVLEN=5529000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample12        chrX    124429000       END=129969000;SVLEN=5540000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample24        chrX    124429000       END=129974000;SVLEN=5545000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample14        chrX    124434000       END=129959000;SVLEN=5525000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample5 chrX    124436000       END=129981000;SVLEN=5545000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample16        chrX    124437000       END=129957000;SVLEN=5520000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.53
Sample25        chrX    124439000       END=129974000;SVLEN=5535000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.52
Sample15        chrX    124440000       END=129955000;SVLEN=5515000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample21        chrX    124441000       END=129981000;SVLEN=5540000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample23        chrX    124442000       END=129967000;SVLEN=5525000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample4 chrX    124446000       END=129976000;SVLEN=5530000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.53
Sample8 chrX    124447000       END=129977000;SVLEN=5530000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.53
Sample17        chrX    124449000       END=129974000;SVLEN=5525000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample13        chrX    124465000       END=129950000;SVLEN=5485000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.49
Sample8 chrX    130027000       END=134352000;SVLEN=4325000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample17        chrX    130063000       END=134403000;SVLEN=4340000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample10        chrX    130066000       END=134346000;SVLEN=4280000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample21        chrX    130076000       END=134381000;SVLEN=4305000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample24        chrX    130078000       END=134358000;SVLEN=4280000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample15        chrX    130079000       END=134349000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample19        chrX    130079000       END=134349000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample4 chrX    130080000       END=134350000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample5 chrX    130080000       END=134350000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample23        chrX    130080000       END=134351000;SVLEN=4271000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample14        chrX    130080000       END=134355000;SVLEN=4275000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample16        chrX    130080000       END=134355000;SVLEN=4275000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.53
Sample12        chrX    130082000       END=134352000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample25        chrX    130082000       END=134402000;SVLEN=4320000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.51
Sample13        chrX    130091000       END=134351000;SVLEN=4260000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.48
Sample21        chrX    134486000       END=144556000;SVLEN=10070000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.49
Sample12        chrX    134496000       END=144424000;SVLEN=9928000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample8 chrX    134511000       END=144501000;SVLEN=9990000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample4 chrX    134526000       END=145186000;SVLEN=10660000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample23        chrX    134541000       END=144606000;SVLEN=10065000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.49
Sample24        chrX    134546000       END=145206000;SVLEN=10660000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.51
Sample17        chrX    134626000       END=144831000;SVLEN=10205000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.5
Sample25        chrX    134762000       END=144537000;SVLEN=9775000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.51
Sample19        chrX    134776000       END=144496000;SVLEN=9720000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample10        chrX    134911000       END=145361000;SVLEN=10450000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE    1/1:0:0:0.49
Sample16        chrX    134916000       END=145416000;SVLEN=10500000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE    0/1:0:0:0.52
Sample13        chrX    134951000       END=144511000;SVLEN=9560000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.48
Sample15        chrX    134976000       END=144556000;SVLEN=9580000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample14        chrX    134986000       END=144486000;SVLEN=9500000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample5 chrX    134995000       END=144486000;SVLEN=9491000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.49
Sample8 chrX    143862000       END=150267000;SVLEN=6405000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.53
Sample25        chrX    143957000       END=150057000;SVLEN=6100000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample15        chrX    143972000       END=150007000;SVLEN=6035000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample16        chrX    144207000       END=149499000;SVLEN=5292000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample24        chrX    144207000       END=150062000;SVLEN=5855000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample4 chrX    144272000       END=149499000;SVLEN=5227000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.52
Sample5 chrX    144297000       END=149499000;SVLEN=5202000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample23        chrX    144322000       END=150267000;SVLEN=5945000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample14        chrX    144327000       END=150282000;SVLEN=5955000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample19        chrX    144327000       END=150407000;SVLEN=6080000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample12        chrX    144332000       END=150047000;SVLEN=5715000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample13        chrX    144333000       END=150438000;SVLEN=6105000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample10        chrX    144357000       END=150157000;SVLEN=5800000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5
Sample21        chrX    144367000       END=149499000;SVLEN=5132000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample17        chrX    144382000       END=150277000;SVLEN=5895000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample19        chrX    149097000       END=153999000;SVLEN=4902000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample12        chrX    149182000       END=153999000;SVLEN=4817000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample4 chrX    149232000       END=153999000;SVLEN=4767000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.47
Sample14        chrX    149442000       END=153999000;SVLEN=4557000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample8 chrX    149457000       END=153999000;SVLEN=4542000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.49
Sample13        chrX    149472000       END=153999000;SVLEN=4527000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.46
Sample16        chrX    149482000       END=153999000;SVLEN=4517000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.51
Sample25        chrX    149487000       END=153999000;SVLEN=4512000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.48
Sample10        chrX    150001000       END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.5
Sample24        chrX    150001000       END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.47
Sample15        chrX    150001000       END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample17        chrX    150001000       END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample21        chrX    150001000       END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample23        chrX    150001000       END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE     1/1:0:0:0.49
Sample5 chrX    150001000       END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE     0/1:0:0:0.5

Have I misunderstood the use of the --ploidy-chr parameter?

Thank you.