Question

How To Write A Perl Script To Call Somatic Variants From A Sample

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Entering edit mode

11.7 years ago

shilpy ▴ 20

Just started learning about NGS, and using samtools to understand the data provided.

Please let me know how can i write a perl script to call somatic variants from a sample and my final output file contains only somatic calls.

perl ngs samtools • 2.8k views

ADD COMMENT • link updated 11.7 years ago by Jorge Amigo 14k • written 11.7 years ago by shilpy ▴ 20

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Hi, you should provide a little more information if you want us to help you. Can you paste an example of the input and of the output that you want to get?

Moreover, please note that some people may get annoyed if you ask for help, without demonstrating that you have at least made an effort. Why don't you post at least some code that you wrote for this task? Even if the code is not working, you should show that you have at least tried to do something, before asking for help here.

ADD REPLY • link 11.7 years ago by Giovanni M Dall'Olio 28k

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Writing a variant caller in perl is a BAD IDEA.

ADD REPLY • link 11.7 years ago by Zev.Kronenberg 12k

score 1 · Answer 1 · 2013-03-22

is not possible to detect somatic variants from an unique list only, because some comparison pattern must be established in order to remove the germline background. a good idea to find somatic variants out is to use trios, where you could easily set filters among them (in perl if you are fond of it, although simple bash scripting would do) to find which variants of the child were not inherited from the parents. have you consider using existing tools to help you on this task, such as GATK's PhaseByTransmission?