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liusihan / seGMM

A new tool to infer sex from massively parallel sequencing data.
MIT License
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Not finding expected karyotype #4

Closed Fred-07 closed 1 year ago

Fred-07 commented 1 year ago

Hello,

With last version of seGMM ( seGMM Version 1.3.0), the tested sample (TESTED) does not get the expected karyotype. Could you please have a look?

sampleid    XH  Xmap    Ymap    SRY
REF1    0.56018 0.0496495   0.00017624  0
REF2    0.180791    0.0252986   0.00143012  61.54
REF3    0.200837    0.0258266   0.00155916  56.79
REF4    0.176552    0.0252715   0.00140477  60.06
REF5    0.157104    0.0251684   0.00141569  62.6
REF6    0.179973    0.0253427   0.00143232  72.99
REF7    0.632147    0.0477415   0.000163191 0.26
REF8    0.171939    0.0254181   0.00142591  65.75
REF9    0.5839  0.048049    0.000159644 0.1
REF10   0.628233    0.0479089   0.000164281 0.35
REF11   0.61651 0.0480117   0.000169902 0.12
REF12   0.195225    0.0253387   0.00141674  62.93
REF13   0.153226    0.0246027   0.0013775   61.54
REF14   0.175623    0.0244415   0.00141424  71.45
REF15   0.1682  0.024997    0.0014438   65.58
REF16   0.582441    0.047484    0.000162764 0
REF17   0.567593    0.0476668   0.000169133 0
REF18   0.160462    0.0250536   0.00145195  69.86
REF19   0.179975    0.0249752   0.00142281  64.08
REF20   0.152258    0.0250918   0.0014587   69.2
REF21   0.610039    0.047799    0.000155557 0
REF22   0.581446    0.0476336   0.000163381 0
REF23   0.49345 0.0476185   0.000170062 0
REF24   0.176152    0.0250276   0.00145093  78.13
REF25   0.152632    0.0250328   0.0014599   77.1
REF26   0.176471    0.0250873   0.00142497  60.22
REF27   0.600421    0.0479277   0.00016732  0
REF28   0.589026    0.0479591   0.000147903 0.52
REF29   0.195596    0.025113    0.00139658  62.83
REF30   0.160156    0.0252084   0.00138417  64.51
REF31   0.593914    0.0479407   0.000161204 0
REF32   0.572717    0.0479095   0.000154813 0
REF33   0.166667    0.0252178   0.00146612  70.87
REF34   0.683277    0.0479677   0.000156438 0
REF35   0.192061    0.0251521   0.00148271  71.55
REF36   0.120166    0.0250938   0.00149181  59.27
REF37   0.551688    0.0480034   0.000174466 0
REF38   0.579632    0.047957    0.000159149 0.26
REF39   0.168691    0.0245416   0.00144508  60.75
REF40   0.611465    0.0469061   0.000166562 0
REF41   0.190476    0.0243483   0.00139228  65.03
REF42   0.604   0.0469817   0.0001798   0
REF43   0.116059    0.0245327   0.00145301  74.46
REF44   0.162483    0.0249835   0.00145839  66.65
REF45   0.603061    0.0475572   0.000179481 0.08
REF46   0.178988    0.0249668   0.00149554  61.11
REF47   0.175031    0.0247872   0.00150849  76.52
REF48   0.184823    0.0248933   0.00151391  66.41
REF49   0.141264    0.0248336   0.00148154  64.29
REF50   0.698686    0.047548    0.000157188 0
REF51   0.176712    0.024932    0.00149047  55.39
REF52   0.168956    0.0289115   0.00210318  53.22
REF53   0.622174    0.0471549   0.000167434 0.25
REF54   0.186164    0.0250368   0.00134935  60.93
REF55   0.713023    0.0475422   0.000169815 0
REF56   0.602988    0.0475499   0.000165187 0
REF57   0.589769    0.0469736   0.000170866 0
REF58   0.59679 0.0465905   0.000179177 0
REF59   0.180952    0.0246199   0.00144054  65.74
REF60   0.195876    0.024432    0.00144619  83.36
REF61   0.577098    0.0466756   0.000185775 0
REF62   0.153543    0.0245183   0.00144294  61.56
REF63   0.626398    0.0473414   0.000150263 0
REF64   0.190962    0.02449 0.00144736  76.02
REF65   0.183252    0.0247332   0.00144229  58.39
REF66   0.150121    0.024727    0.00146718  81.85
REF67   0.55    0.0470563   0.00014597  0.08
REF68   0.550661    0.0469457   0.00016952  0
REF69   0.61792 0.0467609   0.000159144 0.26
REF70   0.193182    0.0247406   0.00140358  68.23
REF71   0.165939    0.0238367   0.00126774  82.69
REF72   0.173797    0.0245525   0.00141164  63.81
REF73   0.167315    0.0245999   0.00143814  62.62
REF74   0.170929    0.0235092   0.00127107  86.2
REF75   0.150993    0.0249772   0.00139506  60.94
REF76   0.195509    0.0246954   0.00144918  65.44
REF77   0.178841    0.0246225   0.00140217  70.28
REF78   0.599119    0.0469657   0.000164189 0
REF79   0.151915    0.0245573   0.00142457  73.39
REF80   0.677751    0.0462417   0.000184888 0
REF81   0.179975    0.0245481   0.00143369  67.29
REF82   0.16624 0.0244902   0.00143978  72.08
REF83   0.16338 0.0245065   0.00135929  67.17
REF84   0.651241    0.046579    0.000201029 0
REF85   0.611111    0.0467115   0.000163516 0
REF86   0.57384 0.0472958   0.000172902 0
REF87   0.54955 0.0469861   0.000168138 0
REF88   0.534205    0.0442486   0.000151005 0
REF89   0.583424    0.0471988   0.000156192 0
REF90   0.553047    0.0473304   0.000198558 0.18
REF91   0.187256    0.0246509   0.00144741  60.64
REF92   0.591684    0.046811    0.000166406 0.07
REF93   0.203704    0.0247383   0.00145694  68.45
REF94   0.174745    0.0246532   0.00145636  60.82
REF95   0.613883    0.0469882   0.000162698 0
REF96   0.182051    0.0244137   0.00145303  68.24
REF97   0.663976    0.0467973   0.000183386 0
TESTED  0.629703    0.0469322   0.00155632  62.02
liusihan commented 1 year ago

What's the expected karyotype for the TESTED sample?

Fred-07 commented 1 year ago

XXY XH and Xmap are typical 'female' values, while Ymap and SRY are typical 'male' values.

liusihan commented 1 year ago

image I have tried the feature file that you posted with the last version of seGMM ( seGMM Version 1.3.0). The predicted karyotype of TESTED sample is XXY, which match the expected karyotype.

Fred-07 commented 1 year ago

Thank you for testing. I was not careful that the reference file in data does not contain anymore the column 'XYratio'.