Perl source files for reformatting Allegro, Merlin and SimWalk2 linkage-analysis output for plotting by nplplot. Perl source for feeding Merlin output into SimWalk2 for the Merlin-SimWalk2 combined option. PDF and html documentation pages for Mega2 Pre-compiled binaries for some platforms. Perl source to create html-formatted Mega2 log and summary files. Perl source code to reformat the output of the HWE program to a table.įolder of awk scripts for creating the old Mega2 format map files. Perl source code to reformat the output of the GEN program to a table. Python script linkage_to_annotated.py to convert linkage-style format files to the new Mega2 format. The last four batch files below: MEGA2.BATCH_pre, MEGA2.BATCH_ped, MEGA2.BATCH_bed, and MEGA2.BATCH_preannotated, run on the equivalent pre-makeped input files and will produce equivalent results.įolder containing output files created by running mega2 on the *.ex files using the batch file.įolder containing output files created by running with mega2 input files, using the batch file .įolder containing output files created by running mega2 on chromosome 5 data using the batch file from the example folder.įolder containing output files created by running mega2 with PLINK PED input files, using the batch file .įolder containing output files created by running mega2 with PLINK binary input files, using the batch file .įolder containing output files created by running mega2 with mega2 input files, using the batch file .īash script for installing Perl scripts and Mega2. The creates output files for the Cranefoot option and the other MEGA2.BATCH.* files create output files for the Mendel option. If you downloaded and unpacked the mega2_v4.8.0_ bundle following the download section ( 8.1↑), you should see a directory named mega2_v4.8.0_src containing the following directories (in bold) or files listed in alphabetical order:ĭirectory containing documentation describing the technical details involved with adding a new output target to Mega2.ĭirectory containing example data and batch files. Mega2’s performance is almost twice as fast as Version 4.7.0 Mega2 now gives you complete control to specify missing values for quantitative and affection phenotypes, both in the input data and for the data that Mega2 will output. Analysis and Mega2 Analysis modes did not correctly carry through non-numeric alleles to their output files. Note: the common SNP major order did not have this problem.īug: S.A.G.E. The voluminous, complete listing of errors and warnings is now only in the Mega2 ERR(or) log file.īug: PLINK Binary file generation in “individual major” order had been wrong and is now fixed. The Mega2 log file now contains essentially what is displayed on the screen during program execution. Reading in VCF format data is now much faster than it was previously. Several issues affecting the performance processing VCF files have been fixed. Mega2 now supports reading imputed data in IMPUTE2 (Oxford) format (genotype/sample). In most cases, in addition to generating appropriately re-formatted files, Mega2 also generates a shell script that will automatically run the desired program.Ĭreation of an HTML summary of the most recent run of Mega2, with links to input and output and log files (See Section 21.8↓).ġ.1 Graphical overview of Mega2 (a bit out of date, from 2013)ĭetailed installation instructions can be found in Section 8↓. The ability to automatically zero out selected genotypes for specific individuals in order to resolve Mendelian inconsistencies (See Section 9.1.4↓). Input support for Variant Call Format (VCF, BCF, compressed VCF) files, including flexible filtering on input (See Section 9.4↓). Input and output support for the widely-used PLINK format files (See Section 9.2↓). Input and output support for Mega2 format files that contain informative header lines and are readable into R (See Section 9.1↓). The ability to simulate genotype errors (See section 12.10↓). The availability of our Genetic Map Interpolator for aiding in constructing genetic maps of markers (See Section 10↓). The ability to run in an automated way using batch files (See Section 23↓). The ability to create custom tracks of results for visualization in the UCSC genome browser (See Section 20↓). The ability to create publication-quality PDF plots of the results using our nplplot R library (See Section 19↓). In addition to the ability to reformat data for a variety of analysis programs, other useful features of Mega2 include:
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