Supplemental data for: Increased mutation and gene conversion within human segmental duplications

Data used for figure generation and analysis in: Increased mutation and gene conversion within human segmental duplications

1. new-assemblies.zip contains all the new assemblies added in this work beyond the HPRC assemblies (Clint PTR, CHM1, HG00514, NA12878, HG03125). All other assemblies used in this analysis are available through the HPRC: assembly_index/Year1_assemblies_v2_genbank.index.
2. all-sample.vcf is a vcf file with all the variant calls used in this analysis. 
3. alignments.zip contains all the syntenic alignments used for analysis. 
4. data.zip contains annotation data and other information used in analysis and figure making. 

Code used in figure making and analysis is on GitHub.

Snakemake pipelines used in the analysis are also on GitHub:

• Assembly alignment and IGC calling: https://github.com/mrvollger/asm-to-reference-alignment
• Variant calling from assembly alignments: https://github.com/mrvollger/sd-divergence
• Analysis of the triplet content of SNVs: https://github.com/mrvollger/mutyper_workflow