Question: How can I detect false positive deletion in the output of Pindel tool?
0
gravatar for Medhat
5.4 years ago by
Medhat8.7k
Texas
Medhat8.7k wrote:

How to detect false positive deletions in the output of pindel tool?

I am using Pindel to have information about large deletion in a genome, 

my approach to extract the information line from the "some_file_name-p_D" and sort the the extracted file by the support column "which gives the number of reads that support the hypotheses of deletion" but I still have a lot of false positive results.

Any suggestion or better approach? 

sequence next-gen genome • 1.9k views
ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Medhat8.7k
0
gravatar for poisonAlien
5.4 years ago by
poisonAlien2.8k
Asgard
poisonAlien2.8k wrote:

You can take a look at filtering parameters explained in varscan2 paper, to reduce potential false positives.

ADD COMMENTlink written 5.4 years ago by poisonAlien2.8k

you are talking about using totally different program  varscan2 instead of Pindel am I right?

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Medhat8.7k
1

No. You can still use the Pindel output. Those filters explained in the paper can be applied to any output. They are just potential sources of false positives, like variant lying in extreme ends of reads, variants with high mismatch quality, strand bias etc.

ADD REPLYlink written 5.4 years ago by poisonAlien2.8k
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