@@ -301,13 +301,13 @@ Name of distance law table plot if hicstuff_distance_plot is true. Default: dist
--hicstuff_distance_out_plot'[Name of distance law plot file]'
```
#### `--filter_pcr`
#### `--hicstuff_filter_pcr`
If true, PCR duplicates will be filtered based on genomic positions Pairs where both reads have exactly the same coordinates are considered duplicates and only one of those will be conserved. Default: false
```bash
--hicstuff_filter_pcr
```
> :warning: **Warning**: if true, `--filter_pcr_duplicates` **must** be false
> :warning: **Warning**: if true, `--filter_pcr_picard` **must** be false
#### `--hicstuff_filter_pcr_out_file`
Name of pair file after PCR filtering. Default: 'valid_idx_pcrfree.pairs'
...
...
@@ -316,11 +316,11 @@ Name of pair file after PCR filtering. Default: 'valid_idx_pcrfree.pairs'
--hicstuff_filter_pcr_out_file'[Name of pcr free pair file]'
```
#### `--filter_pcr_duplicates`
#### `--filter_pcr_picard`
If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If true, `--keep_dups`**must** also be true. Default:'false'
If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If true, `--hicstuff_filter_pcr`**must** be false. Default:'false'