BCFtools filteration criterion (biallelic sites)

[XingzhengLee]

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]

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? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGA4IZIMFZBRZPTTF226ETUP4WS3ANCNFSM5JTNTY6Q>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- 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]

Thank you!