Hi there, I am seeing some differences between the /dev/stdout and -O output.bam output formats for filterSamReads.
GATK version: gatk-126.96.36.199
gatk-188.8.131.52/gatk FilterSamReads -I input.bam -O /dev/stdout --READ_LIST_FILE unmap.wrong.excludes --FILTER excludeReadList --VALIDATION_STRINGENCY SILENT > stdout.bam
gatk-184.108.40.206/gatk FilterSamReads -I input.bam -O output.bam --READ_LIST_FILE unmap.wrong.excludes --FILTER excludeReadList --VALIDATION_STRINGENCY SILENT
When I use the bams that are created, Command 2 gives me a usable bam file, but command 1 gives me errors suggesting a malformed/truncated bam file:
samtools view stdout.bam
[W::sam_read1] Parse error at line 1
[main_samview] truncated file.
samtools view output.bam #works fine
Ideally, I would be able to stream from gatk into a separate command. I tried using the --QUIET parameter to see if the stdout stream was interfered with by logging updates, but that didn't help. Do you have any suggestions?
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