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google / deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
BSD 3-Clause "New" or "Revised" License
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gvcf #18

Closed minw2828 closed 1 month ago

minw2828 commented 2 months ago

Hello,

Thank you for producing the tool. :)

I am wondering why the output includes a gvcf file. How do you think I should use it? Is the gvcf file prepared for the future to detect somatic variants in a large cohort?

Many thanks, Min

kishwarshafin commented 1 month ago

hi @minw2828,

Yes, although the gvcf outputs can be cumbersome it does allow to do cohort level somatic variant analysis if anyone is interested in that. We thought it would be a nice use-case to support so we have GVCF support. It is optional, so if you don't need it, you can turn it off without any issues. Turning it off will improve your runtime.

minw2828 commented 1 month ago

Hi @kishwarshafin,

Thank you! That's helpful.

Is the way to turn off GVCF simply leave out the following line? --output_gvcf=${OUTPUT_DIR}/OUTPUT.g.vcf.gz \ **Path to output gVCF file.

Many thanks, Min

pichuan commented 1 month ago

Hi @minw2828 , Please just remove that line, which should allow you to skip generating the gVCF file.

minw2828 commented 1 month ago

Thank you @pichuan!