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.