How come female has variants in chrY and How come male variants in chrX are represented as two alleles?

Question

[genomicsngs2017]

Hi Friends,

I am a new user to NGS arena. I pasted a couple of vcf records for chrY and chrX from trio analysis.

1) Genotype (GT) for son is 0/1, which is heterozygous. 0 refers to the reference allele and 1 refers to the alternate allele. We get one chromosome from each parent. One parent's chromosome has 0 (same as reference allele) and another parent's chromosome has 1 (different from reference allele).

2) Same with father's genotype

3) Genotype for mother is 1/1, which is homozygous alternate. 1 refers to the alternate allele. So both the parent's chromosome have 1 (different from reference allele).

Is my understanding about the genotype correct?

4) Allele Count - AC : 1 alternate allele from son, 2 alternate alleles from mother and 1 alternate allele from father, so total four(4) alternate alleles. Therefore AC refers to alternate allele count.

5) Total Allele - AN : 2 alleles for son, 2 alleles for mother and 2 alleles for father, so total 6 alleles.

6) Allele Frequency AF: 4/6 is 0.667. So this allele frequency refers alternate allele frequency. Am I correct?

Female doesn't have chromosome Y, so the genotype in chromsome Y should be like this right "nil" ,but how come the mother sample has 1/1 genotype in chrY?

Similarly, for the variants in chrX,

Only mother should have two X chromosomes, so she has 1/1 logically correct. But how come son and father also having 1/1 (two alleles), because male has only one X chromsome that should be represented as "1(one allele)". I am confused about it.

[Pierre Lindenbaum]

some variant callers have no idea of what is a sexual chromosome: e.g: http://gatkforums.broadinstitute.org/gatk/discussion/5228/

[genomicsngs2017]

Thanks Pierre for the link. I read it.

Do they mean, the variants called in chromosome X and Y are not confident calls because of their depth?

How to people calls variants for sex related inherited disease?

[Titus]

Hi, Don't know if it help but yes you can check metric as depth coverage and frequencies of variation. The think is eliminate sequencing errors and align errors. There are 2 possibilities for me : - You got contamination during sequencing or library making - Your sequences are on chr X and Y are not specific of the position and can be aligned on other chromosome

Best