I have started learning the steps in NGS pipeline.
First, using Bowtie, I aligned the fastq sequence file with the reference file and the output was saved as sam file.
bowtie2 -x grch38_1kgmaj -U 24_1.fastq,24_2.fastq -S eg1.sam
The using samtools, sorted the sam file based on coordinates which was saved as bam file.
sort eg1.sam > my_sorted.bam
This bam file was indexed
samtools index my_sorted.bam
Now, I am trying to mark duplicates in this indexed file (using picard tool)
java -jar $EBROOTPICARD/picard.jar MarkDuplicates I=my_sorted.bam.bai O=marked_duplicates.bam M=marked_dup_metrics.txt
I am stuck in this step. I did not get any output. Are the above steps correct or have I missed any step before marking duplicates?