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yangjl / pseudoRef

Make Pseudo-Reference Genome from VCF/BCF
http://yangjl.com/pseudoRef/
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BCFtools filteration criterion (biallelic sites) #2

Open XingzhengLee opened 2 years ago

XingzhengLee commented 2 years ago

Hi,

Thanks for the 'pseudoRef' commitment.

I noticed that you kept only biallelic sites by using '-m2 -M2' parameters in bcftools. bcftools view JRI20_filtered_snps_annot.bcf.gz -m2 -M2 -v snps -Oz -o JRI20_bi_snps_annot.vcf.gz

There are other multiallelic sites in a large population, why do you discard those sites?

yangjl commented 2 years ago

This piece of software was designed to create a new pseudo reference for another genome. Therefore multiallelic sites were not under our consideration.

Best, Jinliang

On Dec 8, 2021, at 4:21 AM, xingzheng li @.***> wrote:

Hi,

Thanks for the 'pseudoRef' commitment.

I noticed that you kept only biallelic sites by using '-m2 -M2' parameters in bcftools. bcftools view JRI20_filtered_snps_annot.bcf.gz -m2 -M2 -v snps -Oz -o JRI20_bi_snps_annot.vcf.gz

There are other multiallelic sites in a large population, why do you discard those sites?

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-- Jinliang Yang, PhD

Assistant Professor 363 Keim Hall Department of Agronomy and Horticulture Center for Plant Science Innovation University of Nebraska-Lincoln Lincoln, NE 68583-0915

XingzhengLee commented 2 years ago

Thank you!