I am running Picard ValidateSamFile on my Bam file and got this error below. How to fix it.

timt99timt99 remoteMember

java -jar picard.jar ValidateSamFile I=KAPALibPrep_cfDNA_B08_S14_sorted.bam.bam MODE= SUMMARY

HISTOGRAM java.lang.String

Error Type Count
ERROR:INVALID_CIGAR 40
WARNING:MISSING_TAG_NM 35183540

I am also getting this error when running CollectAlignmentSummaryMetrics see below:

SAM validation error: ERROR: Read name NB501999:139:HJH2JBGX5:2:12107:11809:20214_2:N:0:TCCGGCGA+TCAGAGCC, Padding operator not between real operators in CIGAR

Please help me fixed this bam file.

Answers

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