20 Core CODIS markers (13 original plus additional 7 CODIS STR Loci added Jan 2017)
Welcome to the official home of STRait Razor — the STR Allele Identification Tool! The current stable version of this program is v3. The complete v3 package can be found below, in .zip format. Updates to this program will be posted to this page as they are created.
Follow us on:
STRait Razor v3
Released in the summer of 2017, STRait Razor v3 expands the functionality of STRait Razor into Windows platforms via a portable compiled language, C++. This redesign of STRait Razor also applies a novel indexing strategy for the approximate “fuzzy” matching necessary to match anchor sequences. Thus, version 3 of STRait Razor reduces time to analysis and expands the potential user base on additional platforms. More details regarding the functionality of STRait Razor v3, as well as the program and all source code, please see the Github page in the link below.
How to cite:
A. E. Woerner, J. L. King, B. Budowle, Fast STR allele identification with STRait Razor 3.0, Forensic Sci Int Genet. 30 (2017) 18-23.
STRait Razor v2s
The flanking region SNP rs771794429 with a global MAF of 0.0088 is now presumed to lie in the forward primer of the locus vWA in the PowerSeq Auto & Y panel based on population data gathered by NIST (personal communication Lisa Borsuk). The 1000 genomes project reported this SNP primarily in individuals of African descent as well as one other population (Peruvians (PEL) at a MAF = 0.005). Novroski et al. (2016) observed this variant in three length-based alleles (13, n =1 or freq = 0.0025; 14, n = 6 or freq = 0.0150; 15, n = 1 or freq = 0.0025) using the ForenSeq DNA Signature Preparation Kit for the African American population with no observations in Caucasian, East Asian, or Southwest Hispanic.
Thus, population samples with potential African ancestry analyzed with PowerSeqv1 config file may not show variation for this locus. Version two of the PowerSeq config file (available soon) will address this locus.
ForenSeq config file updated to version 1.2- Private mutations in HG38 for three loci (D5S818, D20S482, and rs430046), minor allele variant (0.36) in HG38 for one locus (rs2342747), and low frequency variant in one sample (NA19043) in 1kG create potential for private mutations to dropout due to default [1 SNP allowed in the anchor].
Config changelog has been updated with the samples from 1000 genomes that would be affected at the given loci. Only two of these loci have phased SNPs in versions <v1.2.
D5S818 =13 individuals of 2504
D12S291= 1 individual of 2504
These two loci in these individuals will dropout when the default conditions(one SNP allowed) are run with configs prior to v1.2. However, if the allowed SNPs is raised to two, alleles would be reported.
Changelog can be found in the zip file.
ForenSeq config file updated to version 1.1- Reverse strand loci not being reported due to transposed reverse anchors (left<–>right). Config changelog created and placed into downloadable
The downloadable found below contains the Perl script as well as the STRait Razor Analysis (SRA) to visualize the data.
Full Zip File
STRait Razor v2s+ Manual
How to cite:
J. L. King, F. R. Wendt, J. Sun, B. Budowle, STRait Razor v2s: Advancing sequence-based STR allele reporting and beyond to other marker systems, Forensic Sci Int Genet. 29 (2017) 21-8.
-updated locus config file
-added support for each base (i.e., all microvariants) within the allelic range
-updated flanks for CSF1PO, D3S1358;
-added loci: D20S482; D6S1043; D9S1122; DXS10103; DXS10148; DYS387S1; D1S1677; D9S2157
-added locus.config file support for individual kits
-PGM 24 Plex
-updated locus config file
-added ‘allsequences.txt’ file for sequence-based analysis
Excel-based Analysis Files for versions prior to v2s*
Sequence-based Analysis v1.2
In order to utilize the potential sequence variation at each locus, the STRait Razor Analysis workbook was developed. This workbook allows users to take the STRait Razor output and perform more in depth analyses. Data may be exported into a separate sheet for fast compilation of a dataset. Two versions of this file are available**.
The standard edition*** is able to process up to 50k unique sequences and is more suitable for large multiplexes or samples with a high number of unique sequences (i.e., mixtures).
**Note: Choose your own adventure!!! When the standard edition of STRait Razor Analysis is
just not lite enough still too cumbersome for your dataset or the computational capabilities of your computer, apply the following changes to the workbook to reduce processing times.
***Note: The standard edition is now most suitable only for high read depth sequencing (e.g., PowerSeq runs with 100k X coverage). The LITE version is recommended for most applications.
-Added batch processing for 24 samples (read one only) or 12 samples (read one and two)
-Changed Sequence output to a single strand consistent with the locus.config file
-Added the Allele Export tab to give added flexibility
If simple length-based data are desired, STRait RazorGenotyper will convert raw STRait Razor data into a final genotype while also combining reads (if applicable). Data may be exported into a separate sheet for fast compilation of a dataset.
-Added tab ‘Advanced Read Combiner’; allows combination of reads 1 & 2 of mixed samples
STRait Razor Histogram Generator converts RazorGenotyper and Sequence Analysis output into mock electropherograms for easy data visualization.
* RETIRED STRait Razor Histogram Generator
Replacement for SRHG
*Please note these files contain macros that must be enabled for proper functionality. All workbooks are in constant development and feedback is not only desired but expected to improve these workbooks. Any help provided is greatly appreciated. Please address Excel comments to Jonathan.King@unthsc.edu
This page was last modified on November 14, 2019