Insert-Size¶
insert-size¶
Calculate the insert-size of a bam or a set of bams. Bams are estimated by evaluating up to the 99.5th percentile of read insert-sizes. This gives numbers that are very close to Picard but a lot faster.
sc insert-size --header input.bam # One bam
sc insert-size --header *.bam # Multiple bams
Options
--verboseOutput information about progress.--distOutput the frequency distribution of insert sizes.
Output
| median | mean | std_dev | min | percentile_99.5 | max_all | n_reads | n_accept | n_use | sample |
|---|---|---|---|---|---|---|---|---|---|
| 179 | 176.5 | 63.954 | 38 | 358 | 359 | 237 | 101 | 100 | AB1 |
Calculate insert-size metrics on a set of bams.
Benchmark
Below is a comparison of seq-collection with picard:
The results are also very very close:
