However, running Picard tools' ValidateSAMfile gave errors (refer below) in both the CRAM as well as the subsequently converted (to) BAM. Running FixMateInformation gave zero errors after revalidation.
Is anyone else encountering such issues with 1000genomes GRCh38 CRAM files ? What could be the source of these errors ?
Mate negative strand flag does not match read negative strand of mate
Mate alignment does not match alignment start of mate
Mate CIGAR string does not match CIGAR string of mate