diff --git a/WES/README.md b/WES/README.md index 4c95c66dab12d2869ce2f360bd63815e7db18bf5..8d0a2d28ce6a1ba497b9123c7a8c5344b6f5d038 100644 --- a/WES/README.md +++ b/WES/README.md @@ -10,15 +10,17 @@ 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>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` + +`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 +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>