Pindel Somatic Calls?

Question

[richard.deborja]

Does Pindel have a somatic mode for indel calling? I figure I would ask the community before I start making my own post-processing script.

[Danielk]

My custom GATK walker (with build instructions) is now available at github: https://github.com/dakl/gatk

Let me know if you have any issues with it.

[xingyongma]

https://github.com/dakl/gatk was compiled using command:

mvn verify -P\!queue

and external-example-1.0-SNAPSHOT.jar was generated.

But

java -jar ./public/external-example/target/external-example-1.0-SNAPSHOT.jar -T SomaticPindelFilter

reported errors:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version exported):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: SomaticPindelFilter
##### ERROR ------------------------------------------------------------------------------------------

[Danielk]

How did you compile?

I get this, which is the expected output:

$ git clone https://github.com/dakl/gatk.git
$ cd gatk
$ mvn verify -P\!queue
$ java -jar ./public/external-example/target/external-example-1.0-SNAPSHOT.jar -T SomaticPindelFilter

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.2-36-gfe24d6a): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Argument with name '--normalid' (-NID) is missing.
##### ERROR Argument with name '--tumorid' (-TID) is missing.
##### ERROR Argument with name '--variant' (-V) is missing.
##### ERROR ------------------------------------------------------------------------------------------

[xingyongma]

I download the ZIP file，and compile as following as you:

$ cd gatk
$ mvn verify -P\!queue
$ java -jar ./public/external-example/target/external-example-1.0-SNAPSHOT.jar -T SomaticPindelFilter

[INFO] GATK Root .......................................... SUCCESS [  1.023 s]
[INFO] GATK Aggregator .................................... SUCCESS [  0.983 s]
[INFO] GATK GSALib ........................................ SUCCESS [  0.696 s]
[INFO] GATK Utils ......................................... SUCCESS [  1.364 s]
[INFO] GATK Engine ........................................ SUCCESS [  0.465 s]
[INFO] GATK Tools Public .................................. SUCCESS [ 12.864 s]
[INFO] External Example ................................... SUCCESS [  9.591 s]
[INFO] GATK Aggregator Public ............................. SUCCESS [  0.018 s]
[INFO] GATK Tools Protected ............................... SUCCESS [ 10.741 s]
[INFO] GATK Package Distribution .......................... SUCCESS [01:25 min]
[INFO] GATK Aggregator Protected .......................... SUCCESS [  0.014 s]

[xingyongma]

It worked:

git clone https://github.com/dakl/gatk.git

​instead

It is very useful

[Danielk]

Glad it worked - I will look into why the zip is not working.

[Danielk]

I get the same (functional) results when downloading the master.zip, so I won't look into this any further.

[limax]

I wonder if the SomaticPindelFilter tool is currently available in the repo at https://github.com/dakl/gatk.

When I enter the command:

java -jar GenomeAnalysisTK-Klevebring.jar -T SomaticPindelFilter

I get an error message that contains the following line:

##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: SomaticPindelFilter

[tayebwajb]

I am also interested. Could you please release SomaticPindelFilter to the world?

Answer 1

[Danielk]

Edit June 8th, 2019 ( by Kevin Blighe ): this answer (below) is old and now outdated. Latest versions of Pindel can perform somatic indel calling

-------------------------------------------

There's no way to do that in pindel, downstream filtering is required.

I use a couple of filters:

1. Reasonable coverage in T and N (btwn 25-1000) and frequency in normal < 15% (settable on cli).
2. Collect all variant that pass (1).
3. Perform Fisher's exact test comparing ref and alt counts in T and N.
4. Adjust for multiple testing using BH/FDR method.
5. Keep variants with adjusted p < 0.05 (settable on cli).

I've implemented this in a custom GATK walker called SomaticPindelFilter. If you're interested, I could release this to the world.

[volvox]

I'm interested in your filter. How can I get it?

Answer 2

[mdm-two]

The setup is described in the online user manual:

http://gmt.genome.wustl.edu/pindel/current/user-manual.html

There is a also a screencast from Kai Ye:

https://www.youtube.com/watch?v=SQKHXfPSJfE&feature=player_embedded