inst/SequenomMarkers_v2/pop_sample/README.md

In StevisonLab/genotypeR: SNP Genotype Marker Design and Analysis

Genotype Markers With Pop Sample

The VCF file must be unzipped before beginning this pipeline. If you are not on a Mac, use this example:

unzip Pop_sample.vcf.zip

If you are using a Mac, use the GUI unzip.

Make sure the VCF file is in the same folder as the wrapper and script files.

To run the entire pipeline, run the wrapper script on the command line and input the VCF file.

Example for Sequenom:

./Pipeline_rapper_pop_sample.sh Pop_sample.vcf sq

Example for GoldenGate:

./Pipeline_rapper_pop_sample.sh Pop_sample.vcf gg

The test file used is Pop_sample.vcf.

The following steps are run through the wrapper script, but they could be executed separately.

Step 1

The Finding_SNPs_pop_sample.pl script is used to find the SNPs that are at least 100 or 50 bases apart, depending on the platform. It will create a bed file, Pop_Sample_SNPs.txt, that contain the chromosome, start position, and end position for each SNP in that sample.

The wrapper script uses the following command to execute step 1. Example for GoldenGate:

./Finding_SNPs_pop_sample.pl Pop_sample.vcf gg

Example for Sequenom:

./Finding_SNPs_pop_sample.pl Pop_sample.vcf sq

Step 2

The Grandmaster_SNPs_pop_sample.pl script is used to make a file containing the chromosome, start position, end position, and the sequence, which contains 100 bases or 50 bases, the SNP, and 100 or 50 more bases on the other side. The SNP is printed as [REFERNCE/ALTERNATE].

The wrapper script uses the following command to execte step 2.

./Grandmaster_SNPs_pop_sample.pl Pop_sample_SNPs.vcf

StevisonLab/genotypeR documentation built on May 5, 2019, 8 p.m.