# Perform analysis merging my dataset and South America dataset, without subsampling

**URL:** <https://nextstrain.discourse.group/t/perform-analysis-merging-my-dataset-and-south-america-dataset-without-subsampling/384>\
**Category:** General\
**Created:** [March 3, 2021, 11:06am UTC](https://nextstrain.discourse.group/t/perform-analysis-merging-my-dataset-and-south-america-dataset-without-subsampling/384 "2021-03-03T11:06:32Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![fhsantanna](https://avatars.discourse-cdn.com/v4/letter/f/f19dbf/32.png) [@fhsantanna](https://nextstrain.discourse.group/u/fhsantanna)\
**Post date:** [March 3, 2021, 11:06am UTC](https://nextstrain.discourse.group/t/perform-analysis-merging-my-dataset-and-south-america-dataset-without-subsampling/384/1 "2021-03-03T11:06:32Z")

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Hi.  
I have a dataset of 300 local sequences. I would like to do a phylogenetic analysis using the South America dataset as reference ([auspice](https://nextstrain.org/ncov/south-america)). For this purpose, I believe it is not necessary to subsample, because it was already made, isn’t it?  
How could I bypass the subsampling step of the snakemake pipeline?

Thank you.

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**Author:** ![fhsantanna](https://avatars.discourse-cdn.com/v4/letter/f/f19dbf/32.png) [@fhsantanna](https://nextstrain.discourse.group/u/fhsantanna)\
**Post date:** [March 3, 2021, 1:45pm UTC](https://nextstrain.discourse.group/t/perform-analysis-merging-my-dataset-and-south-america-dataset-without-subsampling/384/2 "2021-03-03T13:45:02Z")

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Solved. I included all strains of the fasta in the file “include.txt”.

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**Author:** ![james](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/james/32/11_2.png) [@james](https://nextstrain.discourse.group/u/james)\
**Post date:** [March 8, 2021, 2:01am UTC](https://nextstrain.discourse.group/t/perform-analysis-merging-my-dataset-and-south-america-dataset-without-subsampling/384/3 "2021-03-08T02:01:44Z")

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Nice work. Currently the subsampling steps are rather integral to the ncov pipeline so skipping them would require a few modifications to the Snakefile, but they can be tricked into not removing any sequences by adding all the samples to the include list (as you’ve done) or by setting “dummy” `group_by` and `sequences_per_group` variables (e.g. “country” and “1000000”, respectively).

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**Author:** ![quietjen](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/quietjen/32/713_2.png) [@quietjen](https://nextstrain.discourse.group/u/quietjen)\
**Post date:** [February 24, 2022, 8:53pm UTC](https://nextstrain.discourse.group/t/perform-analysis-merging-my-dataset-and-south-america-dataset-without-subsampling/384/4 "2022-02-24T20:53:01Z")

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Just heard about using `skip_diagnostics: true` in the build configuration file, to skip filtering strains by quality control metrics.

- [Change Log — SARS-CoV-2 Workflow documentation](https://docs.nextstrain.org/projects/ncov/en/latest/reference/change_log.html#v11-3-february-2022)