[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
Loaded 735874 sites across 3366 contigs
Loaded 735874 sites across 3366 contigs
Reads: 0 total, 0 skipped (flags/unmapped), 0 no site overlap
Fragments: 0 total (0 paired, 0 singletons, 0 discordant, 0 orphans)
Sites: 735874 total, 0 with data, 0 output (depth>=10)
Reads: 1322929 total, 178 skipped (flags/unmapped), 81389 no site overlap
Fragments: 718724 total (522638 paired, 10 singletons, 0 discordant, 196076 orphans)
Sites: 735874 total, 37667 with data, 35929 output (depth>=10)