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
Hi Devon,
Anything similar in PERL? Haven't done much coding in python or C. Looking into pysam though.
Probably, I try to stay away from perl, though, so I wouldn't know off-hand.