I need to append the base quality of fastq file into my existing bam file which does not contain OQ.
One option I see making bam to sam and flattening the fastq 4 lines as one-liner to get the matching quality for the aligned reads, is there any parameters in samtools or any other tools readily available to do this?
The bam is generated by Parabricks germline pipeline. Ultimately I need to convert the bam to cram with OQ.
Thanks in advance.