Problems with Mate-Pairs in 1000G CRAM files.
I downloaded the WGS Phase 3 GRCh38 CRAM files from 1000 genomes. I created the reference directory as per their [instructions](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/README_using_1000genomes_cram.
md "instructions") Upon running ValidateSamFile, on the CRAMs as well as the subsequent converted (to) BAMs; I got many errors regarding Mate pairs.
Running FixMateInformation with Add_MC_tag=true fixed the errors, apparently; but I haven't understood what the source of this error is. I asked 1000G but they said they couldn't replicate my error.
GATK version - 4.0.11
Java version - 1.8