From ff3dee557ceb86b49e4a91fc858e4deda6127e3c Mon Sep 17 00:00:00 2001
From: ruobinLiu <45402954+ruobinLiu@users.noreply.github.com>
Date: Mon, 23 Nov 2020 15:41:57 -0600
Subject: [PATCH] Create 02-How to compare two germplasm and how to find
 sequence varients in the interested region.md

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+---
+title: "How to compare two germplasm and how to find sequence varients in the interested region "
+teaching: 10
+exercises: 10
+questions:
+
+- "How to search for sequence variants between two selected germplasm?"
+- "How to view genome within a given region?"
+objectives:
+- "Providing a step by step demonstration on how to"
+keypoints:
+- Log in KnowPulse with your user account before searching.
+---
+
+
+## Restrict the Sequence Variants to polymorphic between your germplasm
+Underneath germplasm, there is a filter to restrict to polymorphic variants. This filter compares two germplasm and only shows variants with different genotypic calls.
+
+For our example, we would select `ILL 8006` in the first drop down and `CDC Milestone` in the second drop-down to see only sequence variants with differing genotypes (i.e polymorphic variants) between these two germplasm.
+Click Search to see the results.
+![Screenshot of main code listing](../fig/gmatrix-poly-region-3.png)
+
+## Restrict to your trait-implicated Region of the Genome
+The second section of the filter criteria available for the genotype matrix allows you to enter the region of the genome you are interested in. Once you click search, the genotype matrix will only show sequence variants found in this region. 
+In our example, the region of interest is `LcChr4:1875000-2075000`. To enter this, we place `LcChr4` for the `Sequence Name`, `1875000` for the start position and 2075000 for the end position.
+![Screenshot of main code listing](../fig/gmatrix-poly-region-4.png)
+
+## Step #5: (Optionally): Restrict to specific variants.
+Say you are interested in a specific set of variants and would like to see that subset. You can enter the specific variant names by expanding the `Additional Filter criteria` section then clicking Search.
+![Screenshot of main code listing](../fig/gmatrix-poly-region-5.png)