Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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

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.


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