I am stuck in one of the preprocessing steps for exome analysis. Created unmapped and sorted bam files from original fastq files. Also, created aligned and sorted bam files. The unmapped and aligned bam files were validated (using validateSamFile command) and the files showed no errors. The unmapped and aligned bam files were merged (https://gatk.broadinstitute.org/hc/en-us/articles/360037056392-MergeBamAlignment-Picard-#--ALIGNED_READS_ONLY). The merged bam file was also validated (ValidateSamFile command) and it shows these following errors:
Error Type Count
How to remove these errors in the merged bam files?
Please sign in to leave a comment.