Regarding the ValidateSamFile command in picard in GATK 2.21.8, command-line:
java -jar $picard ValidateSamFile I=test.sam MODE=VERBOSE
1. I get this warning "ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur." Is there a command-line option to give a FASTA file with the reference genome? I don't see one in the --help information for ValidateSamFile.
2. Why is a missing @RG header line considered to be an error rather than a warning, and why is a missing RG:X tag in an alignment record considered to be a warning? By my reading of the SAM spec, these are optional features and are not included under "Recommended Practice". Contrast with the @HD header record and NM:i tag, both of which "should be present". Also, bwa mem, which seems to be the de facto standard, does not include @RG or RG:X.
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