Hi
Long time I am seeking for which variant caller gives me read depth for tumour and matched normal also Number of variant bases at the position in the tumor sample from called SNVs and indels; I used Strelka but in output .vcf files I can not find these; I need something like this table
> head(mut_data[,c(1,3:9)])
Sample CHROM POS REF ALT Tumor_Varcount Tumor_Depth Normal_Depth
1 CHC2432T chr1 102961055 G A 4 64 62
I read mutect and mutect2 output format but I did not get if I can extract this information if I call SNV and indels by mutect or mutect2
Any suggestion please
Thank you
Long time I am seeking for which variant caller gives me read depth for tumour and matched normal also Number of variant bases at the position in the tumor sample from called SNVs and indels; I used Strelka but in output .vcf files I can not find these; I need something like this table
> head(mut_data[,c(1,3:9)])
Sample CHROM POS REF ALT Tumor_Varcount Tumor_Depth Normal_Depth
1 CHC2432T chr1 102961055 G A 4 64 62
I read mutect and mutect2 output format but I did not get if I can extract this information if I call SNV and indels by mutect or mutect2
Any suggestion please
Thank you