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For both visual inspection of bam files and upstream analysis, it will be great if the realigned bam file can be kept when running the gatk genotyping.
The text was updated successfully, but these errors were encountered:
Thank you for adding the flag. I have an extra request, would it be possible that when the flag is specified the bam file gets also indexed? We usually use the realigned bam files for visual inspection in IGV and that would be useful.
For both visual inspection of bam files and upstream analysis, it will be great if the realigned bam file can be kept when running the gatk genotyping.
The text was updated successfully, but these errors were encountered: