why I have a 1/1 genotype on chromosome X for males

Answered

Shirely

August 22, 2021 10:24

Hi GTAK team:

I just found the male has the 1/1 genotype on the chromosome X. This should not happen theoretically.

a) GATK version used: 4.1.8
b) Exact command used: standard WDL scripts provided by GATK team

If not an error, choose a category for your question(REQUIRED):
b) What does it mean? there are some error on the haplotypecaller step. But I didn't receive any error info related this.

Much thanks

6 comments

SkyWarrior

August 23, 2021 11:10

Edited
Unless you specify ploidy for chromosome X you will get hemizygous segments as homozygous alt. Though PAR's will give you both homozygous and heterozygous calls.
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Shirely

August 23, 2021 11:20
Hey,

Thanks for you answer. But I didn't find the argument to specify ploidy for chromosome X, and only find the --sample-ploidy argument to specify the number of the chromosome.

Could you please send me a link fot that.

Much thanks
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SkyWarrior

August 23, 2021 11:29
You need to call X chromosome Non-PAR region seperately using -L argument and by defining --sample-ploidy 1 in the command line GATK will call Non-PAR variants with monoploidy active. There is no other way of defining it. Make sure that you do not call PAR with --sample-ploidy 1 otherwise you will be missing some important variants.
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Shirely

August 23, 2021 11:38
Thanks a lot.
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Pamela Bretscher

August 23, 2021 12:57
Thank you for providing your input SkyWarrior!
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Layne Sadler

October 31, 2023 14:12
GATK should issue a warning when allosomes are detected without using appropriate ploidy options
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