I have an already aligned .bam file stored in google bucket. I'm trying to retrieve and ummap them to ubam so i will be able to perform all analysis using GATK best practices. When i use gsutil cp gs:url/to/file/in/google/bucket there's an additional .gstmp extension at .bam files from google bucket.
Samtool view tells me that EOF marker is absent;
is this a problem with downloading my .bam files from google bucket or the .bam file that is actually actually corrupted? How will i be able to tell which is which? Any help will be much appreciated.