What allelic fraction is used as a cutoff in calling mutations?

[nilesh-iiita]

Hi,

Where I can get the cutoff percent regarding allelic fraction to calling mutations?

Best regards

[NikdAK]

Hi, the following cutoffs are applied, depending on which filtering option you choose. The default is "hard" (but note that "all" is actually the less stringed filtering). GEN[Tumor].AF >= 0.1 means only mutations with 10% or more used.

if [ $filtering = 'all' ]; then cat $name/results/Mutect2/$name.m2.filt.selected.vcf \ | java -jar $snpeff_dir/SnpSift.jar filter \ "( ( FILTER = 'PASS') & (GEN[Tumor].AF >= 0.05) & \ ( ( GEN[Tumor].AD[0] + GEN[Tumor].AD[1]) >= 5 ) & \ ( ( GEN[Normal].AD[0] + GEN[Normal].AD[1]) >= 5 ) & \ (GEN[Tumor].AD[1] >= 2) & (GEN[Normal].AD[1] <= 1) )" \

$name/results/Mutect2/$name.m2.postprocessed.vcf elif [ $filtering = 'hard' ]; then cat $name/results/Mutect2/$name.m2.filt.selected.vcf \ | java -jar $snpeff_dir/SnpSift.jar filter \ "( ( FILTER = 'PASS') & (GEN[Tumor].AF >= 0.1) & \ ( ( GEN[Tumor].AD[0] + GEN[Tumor].AD[1]) >= 10 ) & \ ( ( GEN[Normal].AD[0] + GEN[Normal].AD[1]) >= 10 ) & \ (GEN[Tumor].AD[1] >= 3) & (GEN[Normal].AD[1] = 0) )" \ $name/results/Mutect2/$name.m2.postprocessed.vcf elif [ $filtering = 'none' ]; then cat $name/results/Mutect2/$name.m2.filt.selected.vcf \ | java -jar $snpeff_dir/SnpSift.jar filter \ "( ( FILTER = 'PASS' ) )" \ $name/results/Mutect2/$name.m2.postprocessed.vcf fi

You can find the steps here: SNV_Mutect2Postprocessing.sh

[nilesh-iiita]

If I am correct you are referring to: echo " -filt, --filtering Set to 'all' (AF >= 0.05, , Variant in Tumor >= 2, Variant in Normal <= 1, Coverage >= 5), 'hard' (AF >= 0.1, Variant in Tumor >= 3, Variant in Normal = 0, Coverage >= 10) or 'none' (no filters). Optional. Defaults to 'hard'."

Thanks

[NikdAK]

Yes