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Why bcftools + guess-ploidy is not giving the correct results

Hi,

I have used bcftools +guess-ploidy on some of the vcf files but every sample is predicted as females. How to correct this? Or any other easy method available to guess the gender based on exome data. Thanks in advance.

bcftools guess-ploidy
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written by nkausthu • nkausthu

We used plink's --check-sex option based on a reliable set of SNPs on chrX and chrY. Not sure how different that would be from the guess-ploidy extension

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written by Ram Ram

I had seen 10k reads aligned to y for a female exome data. I don't know the cutoff for number of reads to consider to be significant or not.

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written by nkausthu • nkausthu

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. This comment belongs under @swbarnes2's.

SUBMIT ANSWER is for new answers to original question.

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written by GenoMax GenoMax

1 answer

Have you confirmed that your samples have significant # of reads aligning to the Y chromosome?

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written by swbarnes2 swbarnes2

I had seen 10k reads aligned to y for a female exome data. I don't know the cutoff for number of reads to consider to be significant or not.

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written by nkausthu • nkausthu

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