Question: Varscan read count output conversion
0
gravatar for shubhra.bhattacharya
13 months ago by
shubhra.bhattacharya120 wrote:

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:

>Eucgr.A01169.1
NNNNNATG[C/T][A/T]

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.

--Thanks

varscan • 367 views
ADD COMMENTlink written 13 months ago by shubhra.bhattacharya120
1

see Construct a combination set of fasta sequences from a vcf

ADD REPLYlink written 13 months ago by Pierre Lindenbaum124k
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