# convert sam to bam, filtering out alignments with less than $MINQ quality
# (I've seen a value of 20 or 30 being used in some cases)
samtools view -hbSq $MINQ pe.sam > tmp.bam
samtools sort tmp.bam tmp.sorted
samtools index tmp.sorted.bam
# remove duplicates (this only works for samtools <= 0.1.20)
samtools rmdup tmp.sorted.bam tmp.rmdup.sorted.bam
# add readgroups
picard-tools AddOrReplaceReadGroups INPUT=tmp.rmdup.sorted.bam OUTPUT=tmp.addrg.rmdup.sorted.bam RGLB="rglib" RGPL="rgpl" RGPU="rgpu" RGSM="rgsm" VALIDATION_STRINGENCY=SILENT
samtools index tmp.addrg.rmdup.sorted.bam
# realign near indels
picard-tools CreateSequenceDictionary R=hg38.fa O=hg38.dict
samtools faidx hg38.fa
# you might want to look for better gatk options
gatk -I tmp.addrg.rmdup.sorted.bam -R hg38.fa -T RealignerTargetCreator -o help.intervals
gatk -I tmp.addrg.rmdup.sorted.bam -R hg38.fa -T IndelRealigner -targetIntervals help.intervals -o final.bam
samtools index final.bam