I have generated vcf files containing SNPs from mutant genome sequences. Since the mutagen only caused transitions to these genomes, I want to make vcf files that have only transition mutations/ SNPs. I know awk could easily do it. I have started with the following command:
cat file.vcf | awk '$4=="G" && $5=="C"' > transitions.vcf
it generates a file with G>C transitions only. However, I need to include 3 other transitions (A>G, C>T and T>C) from the same file to the transitions.vcf file. I am not sure how to combine all awks together to get one single vcf file. Any help is highly appreciated.