Phred-scaled strand bias P-value based on INFO/ADF,INFO/ADR, and INFO/DP4

[Silvia-lme]

I have got warning "bcftools version mismatch .. bcftools at 1.13, the plugin "fill-SP-by-ADF" at 1.12", when I running plugin "fill-SP-by-ADF.c" to obtain Phred-scaled strand bias P-value based on INFO/DP4. Should I use the older bcftools version 1.12 instead of 1.13 to run this plugin?
Thanks.

[pd3]

That just means you are running different version of bcftools than the plugin. Usually this works okay, but it makes sense to use the matching version. The plugins are picked from directory specified by the BCFTOOLS_PLUGINS environment variable

[Silvia-lme]

I recently installed bcftools v1.21 and am very happy with the improvements—thank you for your work!

In previous versions, I used the "fill-SP-by-ADF" plugin to obtain the INFO/FS2 value (Phred-scaled p-value using Fisher's exact test) from INFO/DP4. The transformed tag for FS2 appeared as:
INFO=<ID=FS2,Number=1,Type=Integer,Description="INFO/FS2 based on INFO/DP4">

However, I noticed that this plugin is missing in the latest version. Would it be possible to add it back? If not, could you suggest an alternative method to calculate the Phred-scaled p-value using Fisher's exact test for SNPs?

Thank you.

[pd3]

I searched the history of bcftools plugins and could not find one named fill-SP-by-ADF, so it appears it is not an official bcftools plugin. However, it would not be too hard to extend the plugin fill-tags to do that. Here probably best would be to add a support for a new function in the filtering expressions and access as in this example with DP

TAG:Number=Type(EXPR)                 
           ..  Experimental support for user expressions such as DP:1=int(sum(DP))
               If Number and Type are not given (e.g. DP=sum(DP)), variable number (Number=.) of floating point
               values (Type=Float) will be used.

[Silvia-lme]

Thank you for your advice on how to extend the fill-tags plugin for the new TAG. I will attempt to implement it, and if I encounter any issues, I will reach out to you again. Thank you.

[pd3]

This is now possible, it can be added for example like this

bcftools +fill-tags in.bcf -- -t 'FMT/FT:1=phred(fisher(FMT/DP4))'
bcftools +fill-tags in.bcf -- -t 'FMT/FT:1=phred(fisher(FMT/ADF,FMT/ADR))'

Please try it out and let me know in case of problems, it has not been terribly well tested.