Sequencing Data and Metadata Cross Checks

Validation Script	Validation Rule	Note
c620_submitter_read_group_id_match	Provided submitter_read_group_id matches ID found in BAM header when read_group_id_in_bam not provided.
c630_rg_id_in_bam_match	read_group_id_in_bam matches ID found in BAM header
c650_sm_in_bam_matches_metadata	submitterSampleId matches SM entry in BAM header.
c660_metadata_in_bam_rg_header	The following BAM header fields match metadata payload fields: BC:sample_barcode CN:sequencing_center DT:sequencing_date LB:library_name PI:insert_size PL:platform PM:platform_model PU:platform_unit A warning will produced if differences are detected and info in metadata payload will be prioritized downstream
c670_rg_is_paired_in_bam	Per read_group, verifies provided is_paired_end is concordant with status in BAM files
c680_repeated_read_names_per_group_in_bam	Per first 500,000 entries in BAM, verifies read_name is not duplicated nor exists in another read_group within the same BAM
c681_fileSize_match	Each entry in files's size (bytes) matches size in metadata payload
c683_fileMd5sum_match	Each entry in files's Md5sum matches Md5 in metadata payload