Capturing clusters having T to C mutation

[aevgup]

Hi Everyone,

I have a bed file in the following format

chr7 	29434 	29451 	read 	13
chr7 	61642 	61661 	read 	16
chr7 	99192 	99229 	read 	11
chr7 	115309 	115326 	read 	5
chr7 	134211 	134229 	read 	8
chr7 	216704 	216727 	read 	29
chr7 	289611 	289636 	read 	6
chr7 	348415 	348440 	read 	5
chr7 	385948 	385968 	read 	7
chr7 	395913 	396002 	read 	533

These coordinates represent clusters and 5th column represents number of reads in each cluster.

When I view these coordinates one by one on IGV, I noticed that by default the allele frequency threshold is 0.2(which is exactly what i need)

I want to keep only those clusters in which at a position if ref is T (5'--->3') then in the reads within cluster it is C such that allele frequency threshold of 0.2 is satisfied.

Please see the attached IGV image.

Is there a way to do that?

Is this possible to do with samtools??

Thanks for the help and time.

Regards
Varun