Check if a bam file format is valid

checkBamFormat.txt

ml picard/2.21.6-Java-11.0.2

java -jar \
    $EBROOTPICARD/picard.jar \
    ValidateSamFile \
    I=/gpfs0/scratch/mvc002/testTwoTumors/split_sams_2//S0149_1.sam \
    MODE=VERBOSE
    
    # Can optionally include ignore arguments to ignore specific error types
    IGNORE=MISSING_TAG_NM \
    IGNORE=RECORD_OUT_OF_ORDER
    
See https://broadinstitute.github.io/picard/command-line-overview.html for more possible IGNORE options