Update README.md

WES/README.md

@@ -9,10 +9,28 @@ Below the main steps performed and the relative running commands:
 
 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><summary>Code</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` 
+picard SortSam INPUT=BALL_10_395_3_L1.sam OUTPUT=BALL_12_27_1_L1_mouse.bam SORT_ORDER=coordinate
+picard MergeSamFiles I=BALL_10_395_3_L1_mouse.bam I=BALL_10_395_3_L2_mouse.bam OUTPUT=BALL_10_395_3_mouse.bam
+samtools index BALL_10_395_3_mouse.bam
+picard MarkDuplicates INPUT=BALL_10_395_3_mouse.bam OUTPUT=BALL_10_395_3.dedup_reads_mouse.bam METRICS_FILE=BALL_10_395_3.metrics_mouse.txt
+gatk BaseRecalibrator --input BALL_10_395_3.dedup_reads_mouse.bam --reference $genome --known-sites $vreference --output BALL_10_395_3_recal_data_mouse.table
+gatk ApplyBQSR --reference $genome --input BALL_10_395_3.dedup_reads_mouse.bam --output BALL_10_395_3.dedup_reads_mouse_recal.bam --bqsr-recal-file BALL_10_395_3_recal_data_mouse.table --static-quantized-quals 10 --static-quantized-qual
+gatk BaseRecalibrator --input BALL_10_395_3.dedup_reads_mouse_recal.bam --reference $genome --known-sites $vreference --output BALL_10_395_3_post_recal_data_mouse.table
+```
 </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.  
+## Disambiguation ##
+
+We perform alignment using both human and mouse reference genomes in order to perform reads disambiguation using [disambiguate](https://pubmed.ncbi.nlm.nih.gov/27990269/) and discard reads from human mapping that belong to mouse cells.  
+
+<details><summary>Code</summary>
+`python disambiguate.py -a bwa -s Sample_10_395_3 02-Alignment_human/BALL_10_395_3.dedup_reads_rehead_recal.bam 02-Alignment_mouse/BALL_10_395_3.dedup_reads_mouse_recal.bam`
+</details>
+
+# Variant calling #
+