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.

Similarly for the reads which are mapping to the reverse strand, ref is A and read has G such that at that position allele frequency of 20 % is satisfied.

Is there a way to do that?

Is this possible to do with samtools??

Thanks for the help and time.

Regards
Varun