output.tsv not well sorted

[Jjuj66]

Hi,

I ran AutoMap v1.2, with 2 vcf files, --common and --chrX option. I've noticed that the output.tsv file in not well sorted by the Begin position.

#Chr    Begin   End Size(Mb)
chr2    114204074       115353814       1.15
chr5    130804987       132560051       1.76
chr8    49371142        50469394        1.10
chr11   73507185        74558585        1.05
chrX    2782116 4985215 2.20
chrX    4985295 9404537 4.42
chrX    9414219 49319525    39.91
chrX    49591026    52857711    3.27
chrX    52862903    55145938    2.28
chrX    55146275    62965055    7.82
chrX    62965138    67415295    4.45
chrX    72794567    74583034    1.79
chrX    67415333    72755923    5.34
chrX    74583402    89204206    14.62
chrX    89207472    119469743   30.26
chrX    119471254   131678991   12.21
chrX    131680824   136873868   5.19
chrX    136874416   141007457   4.13
chrX    144085451   149596554   5.51
chrX    141111645   144078700   2.97
chrX    153605174   155469854   1.86
chrX    150215170   153605159   3.39

In this example, the line chrX 74583402 89204206 14.62 is after the line chrX 67415333 72755923 5.34. Same with chrX 141111645 144078700 2.97 and chrX 144085451 149596554 5.51.

I do not know if it's related with chrX. It's seems not to be important but still, I was confused at first.

Another question how the tools know if a sample is female or male ?

Best, Julien

[mquinodo]

Dear Julien,

Thank you again for your feedback. I corrected the sorting issue. The tools does not know the sex and analyse the samples agnostically.

Best, Mathieu