remove_duplicates.sub

#!/bin/bash -x
#SBATCH --job-name=remove_dups
#SBATCH --account=kgidiotis
#SBATCH --output=/home/kgidiotis/minimap_pipeline/errors/picard_remove_dups_%j.out
#SBATCH --error=/home/kgidiotis/minimap_pipeline/errors/picard_remove_dups_%j.err
#SBATCH --cpus-per-task=8
#SBATCH --mem=50G
#SBATCH --partition=fatnodes

# Author: MSc Kostas Gidiotis
# Group: Laura Botigue's group 
# Date: 05-01-2024
# Description: 
# 	This script is removing the PCR duplicates from the generated bwa bam files
# 	*long read sequencing data for Wild Emmer Wheat* 
# Prerequisites: 
#	long read sequencing bam files 
# Output: 
# 	bam files with PCR duplicates removed 
#Note:
# 	Check after you have generated the new bam(PCR dups removed) the flagstats (before - after)

# Load the picard module
module load picard/2.22.3
module load samtools
# Directory path containing the BAM files
INPUT_DIR=/scratch/125-emmer/free-threshing/long_read_outputs/minimap2_wild_emmer/minimap2_South_I100g

# Path/InputFile manually
INPUT_FILE=/scratch/125-emmer/free-threshing/long_read_outputs/minimap2_wild_emmer/minimap2_South_I100g/WHPBRVajis20231024-2045_sorted.bam

FILENAME=$(basename -- "$INPUT_FILE")
FILENAME_NOEXT="${FILENAME%_*}"
echo $FILENAME_NOEXT

java -jar $PICARDPATH/picard.jar AddOrReplaceReadGroups \
      I=$INPUT_DIR/${FILENAME_NOEXT}_sorted_dupMarked.bam \
      O=$INPUT_DIR/${FILENAME_NOEXT}_sorted_dupMarked_RG.bam \
      RGID=read_group_id \
      RGLB=LibraryPlaceholder \
      RGPL=PACBIO_SMRT \
      RGPU=unit1 \
      RGSM=$FILENAME \
VALIDATION_STRINGENCY=SILENT

#LibraryPlaceholder
# index dupMarked file 
samtools index -c $INPUT_DIR/${FILENAME_NOEXT}_sorted_dupMarked_RG.bam                                                

java -Xmx32g -jar $PICARDPATH/picard.jar ValidateSamFile I=$INPUT_DIR/${FILENAME_NOEXT}_sorted_dupMarked_RG.bam \
MODE=SUMMARY VALIDATION_STRINGENCY=SILENT

# Run the picard MarkDuplicates command
java -Xmx100g -jar $PICARDPATH/picard.jar MarkDuplicates \
  VALIDATION_STRINGENCY=SILENT \
  I=$INPUT_DIR/${FILENAME_NOEXT}_sorted_dupMarked_RG.bam \
  O=$INPUT_DIR/${FILENAME_NOEXT}_sorted_dupRemoved_RG.bam \
  M=$INPUT_DIR/metrics_${FILENAME_NOEXT}.txt \
  REMOVE_DUPLICATES=true

samtools index -c $INPUT_DIR/${FILENAME_NOEXT}_sorted_dupRemoved_RG.bam

# unload the module 
module unload picard/2.22.3	
module unload samtools
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