Hi all, I need to append the base quality of fastq file into my existing bam file which does not contain OQ. Other than making bam to sam and flattening the fastq 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. This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.
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