I am trying to filter .vcf files to contain only single point SNP and remove indel.
I have remove indel from the .vcf file by using the following command:
grep -v $'\t-\t' in.vcf > no_indels.vcf
I am able to remove indel from .vcf file.
But I also want to remove any SNP corresponding to CAT --> C and C --> CTATGG
I just want my .vcf file to contain only A-T, or T-A or G-C.
I mean just one single point mutation only.
Can anyone please help me with this?