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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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it's suitable for target panel sequencing ? #12

Open WinterLi1993 opened 6 years ago

WinterLi1993 commented 6 years ago

hi, my data is cfDNA data from target panel sequencing with high coverage . so Pisces is Ok for my data to call somatic mutation with tumor only sample ？？

thank you in advance !

tamsen commented 6 years ago

Hi,

Yes, absolutely! It should be fine. If you are going to look for variants that are less that 1% of the sample mixture, you will not want the default settings, though. The defaults are configured to call down to 1% on basecalls that are mostly > Q20

Defaults: MinVariantQScore 20 MinBaseCallQuality 20 NoiseLevelForQModel 20 MinimumFrequency 0.01

If you are going to look for 0.1% variants (for example, or lower) you may have to modify these parameters:

MinVariantQScore 20 (raise or lower this to let through more or less variants, might depend on your assay quality) MinBaseCallQuality 20 (raise this if you have high enough base call quality to still get coverage) NoiseLevelForQModel 30 (or higher, as needed) MinimumFrequency 0.001 (or lower, as needed)

If you need more info:

the FAQ, https://github.com/Illumina/Pisces/wiki/Frequently-Asked-Questions "Can we get a version of the somatic caller with the hard coded lower detection threshold of 1% reduced or removed?"

https://github.com/Illumina/Pisces/wiki/Pisces-5.2.5-Supported-Options

https://github.com/Illumina/Pisces/wiki/Suggested-Pipeline-Configuration-5.2.5

WinterLi1993 commented 6 years ago

thank you . why not use python to implement Pisces ? sometimes to install dotnet ,root power is needed ...

WinterLi1993 commented 6 years ago

@tamsen ./bin/dotnet: /usr/lib64/libstdc++.so.6: version GLIBCXX_3.4.14' not found (required by ./bin/dotnet) ./bin/dotnet: /usr/lib64/libstdc++.so.6: versionGLIBCXX_3.4.15' not found (required by ./bin/dotnet)

I have no root power ,how to solve that ?

tamsen commented 6 years ago

Re root: Perhaps ask your sysadmin?

Re Why not Python: that's a fair question. If we were starting again from scratch, perhaps I would. But I’m pretty language agnostic. IMHO, most modern languages are fine and somewhat converging. Pisces is in C# because it started life running natively on a Miseq PC, where it swam with all the robot code and instrument control software, also in C# at that time.