Update README.md

WES/README.md

@@ -11,7 +11,7 @@ Fastq files were aligned with [BWA aligner](https://github.com/lh3/bwa) (v0.7.17
 
 ```
 - bwa mem -t 12 -R @RG\tID:SampleID_L1\tSM:SampleID  PL:ILLUMINA -M GRCh38.p13.genome.fa 3_S8_L001_R1_001.fastq.gz 3_S8_L001_R2_001.fastq.gz` 
-- picard SortSam INPUT=SampleID_L1.sam OUTPUT=BALL_12_27_1_L1_mouse.bam SORT_ORDER=coordinate
+- picard SortSam INPUT=SampleID_L1.sam OUTPUT=BALL_12_27_1_L1_mouse.bam SORT_ORDER=coordinate # both lanes L1 and L2
 - picard MergeSamFiles I=SampleID_L1_mouse.bam I=SampleID_L2_mouse.bam OUTPUT=SampleID_mouse.bam
 - samtools index SampleID_mouse.bam
 - picard MarkDuplicates INPUT=SampleID_mouse.bam OUTPUT=SampleID.dedup_reads_mouse.bam METRICS_FILE=SampleID.metrics_mouse.txt