Generate samtools stats with Standard Flags (_F0x900.stats, _F0xB00.stats) for Illumina Data QC

[sainsachiko]

Description of feature

To ennsure that samtools stats is being run on Illumina data with the appropriate filtering flags, in line with NPG practices.
This helps exclude unwanted reads (e.g., secondary, supplementary, or QC-failed) and standardizes QC metrics across datasets.
Context: NPG typically runs samtools stats multiple times using different flags. At a minimum, the -F 0xB00 flag should be applied to exclude: Secondary alignments (0x100) Supplementary alignments (0x800) Fails vendor quality checks (0x200)