GATK for microbes
I have read a lot about variant calling using GATK especially Mutect2. But no where, even in the pipeline or even good practise documentation for microbes variant calling have i noticed any sort of filters to be used for variant filtering for SNPs and INDELs. I am new to the field of bioinformatics and i was looking for some guidance on choosing filters for both and i have noticed that people who work with human data have set different filters for both SNPs and INDELs. But those filters work only with vcf files generated by Haplotypecaller and Mutect2 has different heading in the format. I'm stuck in the step of filtering by snp and indels file.
Thanks.
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We have a github repository and dockstore repository for microbial variant calling.
You may be able to checkout wdl workflows from the links below
https://github.com/broadinstitute/GATK-for-Microbes
Once you try out if you have any questions let us know so we can take a look at it.
Regards.
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Hello @Gökalp Çelik
Thank you for the suggestion!
I have tried this workflow. The main problem i encountered was that i was to apply filter ( i think it was for MQ or something similar ) and the vcf file generated by mutect2 doesnt have it, so i had to switch to Haplotypecaller. Even though it's not suggested to use for bacterial genome but i changed the --sample ploidy to 1, not sure if that would make a lot of difference while handling bacterial genome.
Further suggestions are most welcomed.
Regards.
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HaplotypeCaller and Mutect2 use different set of annotations therefore filtering methodologies are not similar. Mutect2 uses FilterMutectCalls primarily therefore it has its own filtering models. Using --microbial-mode parameter during FilterMutectCalls step is specifically crafted for this purpose.
We do not recommend using HaplotypeCaller for microbial calling since impurities and intra-sample variation will cause unexpected variant calls which may not really reflect correctly what is inside the sample you have.
I hope this helps.
Regards.
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I will work on the suggested pipeline and let you know. Also, does Funcotator annotate bacterial genome? If not, which other annotating tool is compatible with mutect2 vcf format ?
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We may not have the proper annotation sources pre-compiled for your organism of interest therefore you may need to create your own or you may use other annotation sources such as snpeff, VEP etc. many of which contain pre-compiled sources for functional and ontological annotations.
I hope this helps.
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