test readme WES

WES/README.md

+## Introduction
+
+**Whole Exome ** data analysis - from fastq data to variants calling and annotation
+As stated in supplementary methods we performed WES analysis relying mostly on the GATK best practices for WES analysis.
+
+Below the main steps performed and the relative running commands:
+
+# Alignment #
+
+Fastq files were aligned with [BWA aligner](https://github.com/lh3/bwa) (v0.7.17) to GRCh38 reference genome (GRCh38.p13 gencodegenes) using default parameters, except for the -M option for [Picard](https://broadinstitute.github.io/picard/) compatibility necessary for marking of duplicates.  
+
+<details><summary>Click to expand</summary>
+`bwa mem -t 12 -R @RG\tID:BALL_10_395_3_L1\tSM:BALL_10_395_3  PL:ILLUMINA -M GRCh38.p13.genome.fa 3_S8_L001_R1_001.fastq.gz 3_S8_L001_R2_001.fastq.gz`
+</details>
+
+We perform alignment using both human GRCh38 and mouse GRCm38 reference genomes in order to perform reads disambiguation and discard reads from human mapping that belong to mouse cells.  
+
+