Incorrect CNV calculation of chrX and chrY

[ywzhang071394]

Hi,

Thank you for the nice tool!
I am recently using Hatchet to investigate CNV and WGD. We ran the regular pipeline for a female sample, which generated bulk.bb.withxy. And we used this file to compute-cn. However, in the output chosen.diploid.seg.ucn file, we saw both chrX and chrY, as shown in the below. Was the CN calculation of chrX influenced by the inclusion of chrY? How can we correct it?
Thanks!

#CHR START END SAMPLE cn_normal u_normal cn_clone1 u_clone1 cn_clone2 u_clone2
chrX 1 58100001 tumor 1|1 0.26391822 1|0 0.6360825 3|0 0.099999283
chrX 63800000 154259567 tumor 1|1 0.26391822 1|0 0.6360825 3|0 0.099999283
chrY 1 10300001 tumor 1|1 0.26391822 1|0 0.6360825 3|0 0.099999283
chrY 10600000 62460030 tumor 1|1 0.26391822 1|0 0.6360825 3|0 0.099999283

Also, I took a look into the Male sample and was also confused of the output file. As shown in the below table, how can we explain the 1|1 of chrX/chrY in cn_normal? This is a male sample, chrX should be 1|0 ?

#CHR START END SAMPLE cn_normal u_normal cn_clone1 u_clone1 cn_clone2 u_clone2 cn_clone3 u_clone3
chrX 1 58100001 tumor 1|1 0 1|0 0.25199166 6|0 0.19515755 1|0 0.5528508
chrX 63800000 154259567 tumor 1|1 0 1|0 0.25199166 6|0 0.19515755 1|0 0.5528508
chrY 1 10300001 tumor 1|1 0 1|0 0.25199166 6|0 0.19515755 1|0 0.5528508
chrY 10600000 62460030 tumor 1|1 0 1|0 0.25199166 6|0 0.19515755 1|0 0.5528508