Question: Why bcftools + guess-ploidy is not giving the correct results
0
gravatar for nkausthu
8 months ago by
nkausthu20
nkausthu20 wrote:

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.

guess-ploidy bcftools • 354 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by nkausthu20

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

ADD REPLYlink written 8 months ago by RamRS25k
0
gravatar for swbarnes2
8 months ago by
swbarnes27.4k
United States
swbarnes27.4k wrote:

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

ADD COMMENTlink written 8 months ago by swbarnes27.4k

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.

ADD REPLYlink written 8 months ago by nkausthu20
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