Hello all, I have the output of VarScan read count as follows:
Eucgr.A01169.1 6 A 26 25 A:25:2:40:1:24:1:0 Eucgr.A01169.1 7 T 26 20 T:20:2:40:1:19:1:0 Eucgr.A01169.1 8 G 26 18 G:18:2:41:1:17:1:0 Eucgr.A01169.1 9 C 29 25 C:23:1:39:1:23:0:0 T:2:2:54:1:1:1 Eucgr.A01169.1 10 A 31 27 A:25:1:39:1:25:0:0 G:2:1:52:1:2:0
I want to convert this to fasta format such that it is as follows:
The N's represent that the bases have not been covered in this case the first 5 bases. Within the square brackets there is [Ref/Alt] allele.
Can someone tell me if there is a tool or package to help with this.