large number of doublets and AMB calls with demuxlet

[bpuzek]

We are trying to run demuxlet with 8 individuals, using the suggested --alpha 0 --alpha 0.5 parameters

We are getting 82% ambiguous calls, 13% doublets and 5% singlets.

As discussed in one of the issues in demuxlet, this can be due to insufficient number of SNP-overlapping reads "due to various reasons". We obtained our .vcf files from bulk RNA-seq data. Would you expect this to be a problem or would you try and change alpha or another parameter?

Many thanks in advance

[hyunminkang]

Using VCFs from bulk RNA-seq data is not recommended, and it requires a very careful filtering process. The reason could be (1) ambient RNAs (2) problems in identifying informative sites in VCF (usually common coding SNPs), (3) problems in the genotype processing, (4) lack of informative reads. Hyun.

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On Thu, Jan 13, 2022 at 7:21 AM bpuzek ***@***.***> wrote: We are trying to run demuxlet with 8 individuals, using the suggested --alpha 0 --alpha 0.5 parameters We are getting 82% ambiguous calls, 13% doublets and 5% singlets. As discussed in one of the issues <statgen/demuxlet#29> in demuxlet, this can be due to insufficient number of SNP-overlapping reads "due to various reasons". We obtained our .vcf files from bulk RNA-seq data. Would you expect this to be a problem or would you try and change alpha or another parameter? Many thanks in advance — Reply to this email directly, view it on GitHub <#51>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABPY5OIC2N7EX6BEPPGURPTUV27VBANCNFSM5L3VT7BA> . 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>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>