[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
Loaded 735874 sites across 3366 contigs
Loaded 735874 sites across 3366 contigs
Reads: 16436 total, 1694 skipped (flags/unmapped), 14742 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: 5264907 total, 3531 skipped (flags/unmapped), 684213 no site overlap
Fragments: 2356519 total (2220644 paired, 29 singletons, 0 discordant, 135846 orphans)
Sites: 735874 total, 206893 with data, 72377 output (depth>=10)