Update README

README.md

@@ -10,16 +10,17 @@ Snakemake Workflow for Variant Calling
 This is a GATK variant calling snakemake pipeline written by Sherine Awad. 
 
 
-We are using GATK4 GVCF mode. To run the pipeline, edit the config file to match your samples file name and reference genome. 
-Your samples names should be listed by default in samples.tsv file. You can change this file name in *config file* if neededi by editing the **SAMPLES** entry in the config file.
+We are using GATK4 GVCF mode. To run the pipeline, edit the *config file* to match your samples names and other parameters. 
+
+Your samples names should be listed by default in **samples.tsv** file. You can change this file name in *config file* if needed by editing the **SAMPLES** entry in the *config file*.
 
 The pipeline expects samples with suffix ".r_1.fq.gz" and ".r_2.fq.gz" if samples are paired-end.
 Any prefix before this suffix is the sample name and to be written in the "samples.tsv". For single-end reads, the samples suffix is ".fq.gz" and any prefix before this suffix is written in the **"samples.tsv"**.
 For example, if your sample name is sample1.s_1.r_1.fq.gz, then your sample name in the samples file should be sample1.s_1. 
 
-You need to update the config file with whether your samples are paired-end or single reads. If your samples are paired-end, then the **PAIRD** entry in the config file should be set to TRUE, otherwise, set the **PAIRED** entry in the config file to FALSE. You can change the **samples.tsv** name in the config file. 
+You need to update the *config file* with whether your samples are paired-end or single reads. If your samples are paired-end, then the **PAIRD** entry in the config file should be set to TRUE, otherwise, set the **PAIRED** entry in the config file to FALSE. You can change the **samples.tsv** name in the *config file*. 
 
-You need to update your interval list, by editing the **intervals.list** file to list only the chromosomes of interest. You can change the name of this file by editing the config file entry INTERVALS. 
+You need to update your interval list, by editing the **intervals.list** file to list only the chromosomes of interest. You can change the name of this file by editing the *config file* entry **INTERVALS**. 
 
 The pipeline pulls automatically the resources needed by GATK from Broad Institute resource bundles. 
 The pipeline uses **Annovar** for annotations.