I called mutation using Strelka2 with or without the rna flag on RNAseq data. The sample has two missense mutation (on the same gene) which we're sure should show up in the results (gene symbol: BAD , mutations: Ser112Ala & Ser136Ala). When I omit --rna flag, both mutations shows up (see row 1519 & 1520 of the attached annotated "JMG7.ann.PassMissense.vcf.xlsx" output), but with --rna flag, only the first mutation show up (see row 507 of the other attached annotated "JMG7.rna.ann.PassMissense.vcf.xlsx" output). My question is, is it okay to call mutations on RNAseq data without --rna flag given that this option gave us the expected result? As a side question, what does it mean if the two missense mutation appear on the same amino acid on the same sample (for example, see row 508 & 509 in "JMG7.rna.ann.PassMissense.vcf" where Ser155 is mutated to Gly or Thr)?
I called mutation using Strelka2 with or without the rna flag on RNAseq data. The sample has two missense mutation (on the same gene) which we're sure should show up in the results (gene symbol: BAD , mutations: Ser112Ala & Ser136Ala). When I omit --rna flag, both mutations shows up (see row 1519 & 1520 of the attached annotated "JMG7.ann.PassMissense.vcf.xlsx" output), but with --rna flag, only the first mutation show up (see row 507 of the other attached annotated "JMG7.rna.ann.PassMissense.vcf.xlsx" output). My question is, is it okay to call mutations on RNAseq data without --rna flag given that this option gave us the expected result? As a side question, what does it mean if the two missense mutation appear on the same amino acid on the same sample (for example, see row 508 & 509 in "JMG7.rna.ann.PassMissense.vcf" where Ser155 is mutated to Gly or Thr)?
JMG7.rna.ann.PassMissense.vcf.xlsx JMG7.ann.PassMissense.vcf.xlsx