docs: logan caller notes

docs/user-guide/tool_comparisons.md

@@ -0,0 +1,43 @@
+# LOGAN Tools and Tools Tested
+
+
+## SNV
+| Tools |Pros | Cons | Used in Logan|
+|----|---|---|---
+|Mutect2     |Part of GATK best practices| | x |
+|Strelka     | Fast|  Paired only|x|
+|Muse     | Fast|  Paired only, can't be parallelized|x|
+|Lofreq     | Low frequency variants|  Slow,Paired only|x|
+|Vardict | Fast | Lower accuracy|x|
+|Varscan  | Fast| Lower accuracy|x||
+|Octopus | Accurate| Slow,High memory|x|
+|Deepsomatic|Relatively fast|Trained on human data|x|
+
+
+## Structural Variants
+| Tools |Pros | Cons | Approach| Used in Logan|
+|----|---|---|---|---|
+|Manta     |Accurate, fast| |graph-based| x | 
+|SVABA     | Deletion detection||local assembly+ multiple alignment|x|
+|GRIDSS     | Provides blacklist|  Slow, part of HMFtools pipeline|Break end assembly (discordant +split)|x|
+
+Manta, GridSS, and SvABA are based on read-pairs, split-reads, and local-assemblies.  
+References [Joe et al](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10239-9)
+
+## Copy Number
+
+| Tools |Pros | Cons | Used in Logan|
+|----|---|---|---|
+|Purple     |Complete workflow|Doesn't support mm10, requires SV,SNV calls as well | x |
+|Sequenza     | Purity/Ploidy||x|
+|FREEC | Fast | No Purity/Ploidy Estimatation|x|
+|ASCAT  | Fast, Purity/Ploidy| |x|
+|CNVkit |Fast | No Purity/Ploidy Estimatation|x|
+|PureCN|Tumor only|Needs Panel of Normals on Sequencing|
+
+
+
+## Germline
+| Tools |Pros | Cons | Used in Logan| 
+|----|---|---|---|
+|Deepvariant     |Fast, most accurate| Model trained on human genomes (May not support mm10)| x|