Pooled sequecing as Somatic-Germline analysis

[milly]

Hey,
I have a selection experience where I evolved my animals through 3 generations (there are clear phenotipyc difference in the 3rd generation - so the selection originated 2 sublines).

1. there is an available reference genome online.
2. I have their founder population (F0) genome (sequenced 10 animals individually - 10 fastq files → 10 bam files).
3. each subline (line 1 & line 2) was sequences iin a pooled format, where i have 20 animals per pool - so I hav 2 pools (1 per line) with low coverage → 2 bam files.

My question: I want to see what genomic changes are there in the line 1 and line 2. Taking into the account already present differences found n the F0.

Is it possivbe and logic to do varscan somatic? Where I assume the F0 are normal and the subline (line 1 and line 2) will be seen as tumor lines.
What can I do ?

Thank you in advance
Best for all you.

[jennaj]

Welcome @milly

We have tutorials available that can get you started, please see →

• Variant Analysis / Tutorial List

This one seems to be the most similar to your experiment. →

• Hands-on: Identification of somatic and germline variants from tumor and normal sample pairs / Identification of somatic and germline variants from tumor and normal sample pairs / Variant Analysis

If you are completely new to Galaxy, then starting with a tutorial or two to learn how to navigate the interface is a good idea!

• All introduction. → Introduction to Galaxy Analyses / Tutorial List
• Interpreting formats. → Hands-on: NGS data logistics / NGS data logistics / Introduction to Galaxy Analyses
• Basic manipulations and workflows. → Hands-on: Galaxy Basics for everyone / Galaxy Basics for everyone / Introduction to Galaxy Analyses
• Read QA and mapping short introductions. → Sequence analysis / Tutorial List

And finally, to load your reference data into Galaxy and prepare it for use with tools and workflows, please see this FAQ.

• FAQ: How to use Custom Reference Genomes?
• Example topic here with a custom-genome example → Getting NCBI Reference genome indexed for tools: custom genome, reference genome, reference annotation

Hope this helps and you can ask follow up questions!