Question: How can I convert heterozygous genotype data to missing data?
0
gravatar for recycled8345
20 months ago by
recycled83450 wrote:

I want to remove heterozygous genotype data in multi-samples VCF. At first I used bcftools filter -e option, but it made output VCF that lots of sites are deleted because of few heterozygous genotypes. I think this result is not suitable to search valid SNPs. Therefore, I want to convert heterozygous genotype data to missing data for filteration using vcftools later. Could you recommend effective tools?

ADD COMMENTlink modified 20 months ago by finswimmer13k • written 20 months ago by recycled83450

You have not explained very well what you want to do. Can you show the commands that you have already used, and state what is the purpose (in your mind) of each command?

ADD REPLYlink written 20 months ago by Kevin Blighe61k
0
gravatar for finswimmer
20 months ago by
finswimmer13k
Germany
finswimmer13k wrote:

You can do this using the bcftools plugin setGT:

$ bcftools +setGT input.vcf -- -t q -i 'GT="het"' -n "./." > output.vcf

But Kevin's questions persists: Why do you think this is useful?

fin swimmer

ADD COMMENTlink written 20 months ago by finswimmer13k
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