I annotated the flanking regions of SNV mutations with vcftools fill-fs tool. In example;
20 10639675 . C G . . Callers=broad,dkfz,muse,sanger;NumCallers=4;VAF=0.3571;repeat_masker=L1M5;t_alt_count=25;t_ref_count=45;Variant_Classification=Intron;FS=t[C/G]c
it added FS=t[C/G]c where;
- T is the 5prime flanking base and C is the 3 prime flanking base.
- C is the reference and G is the alternated base.
I would like to subset mutations which are similar to followng pattern.
N[T/A]G or C[A/T]N
If you can answer my question by using bcftools/vcftools, it would be very good but I am okay with any other solutions. I know bcftools view -i has a filter option but I couldnt figure it out.
Thank you very much for your help,