Entering edit mode
16 months ago
ttom
▴
220
Hi,
I am trying to use bcftools guess-ploidy
to check gender.
This is how I tried to use it
bcftools view sample.vcf.gz -r chrX:2699521-154931043 | bcftools +guess-ploidy >guess_ploidy.output
The VCF has around 50 samples data from Whole Genome Sequencing and has data on all chromosomes.
However I am getting most of the output for samples not as expected. It cannot be wrong for most of the samples.
Thanks
I used to following command
If I do not use
const-fid
, it was giving the error ``` Error: Multiple instances of '_' in sample ID. If you do not want '_' to be treated as a FID/IID delimiter, use --double-id or --const-fid to choose a different method of converting VCF sample IDs to PLINK IDs, or --id-delim to change the FID/IID delimiter.However I am getting all of the samples listed as females. Should I run this command just on chrX and chrY ?
Running will all the chromosomes is usually not a problem in checking/determining the gender.