Sunday, July 5, 2015

Y-STR Kit

Y-STR Kit will analyse .BAM raw data file or VCF files and outputs in HTML file format with all Y-STR values. It supports build 37 (hg19). If you are selecting VCF file, it must have SNPs/indels and all confident sites (not just the variants). Currently supports FTDNA 111 Y-STR Markers.

The tool provides the following output,
  • Y-STR_Report.html - Output HTML Report
  • bam_chrY.vcf.gz - VCF output with Indels, SNPs and all confident sites.
Prerequisites: 
Usage:

Extract the download and click 'Y-STR Kit UI.exe'. Select the .BAM or VCF file and click ' Analysis'. After clicking ''Execute', a command prompt will automatically open and start executing series of commands.

User Interface

Y-STR Report

Y-STR Report

After a few minutes to several hours, the output will be available inside a subfolder called 'out'.

Download:  Y-STR Kit.zip (76 MB)

Configuration Guide: Y-STR Kit Guide.pdf

Source Code:
Located at 'src' folder and/or uploaded to GitHub

License: The download bundles the following software for pre-processing BAM and VCF files. So, if you are using this tool for non-commercial and/or personal use, you should be alright.
For  my binary and source code, you can use MIT License.

References:
  • Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. [Pubmed]
Change Log :1.1
  • Bug Fix - Unable to load BAM from folders with spaces fixed.
Change Log :1.0
  • FTDNA 111 Y-STR Markers