downsample
Usage
bip downsample [-h] --sample_id SAMPLE_ID --r1 R1 --r2 R2 --out-path OUT_PATH --reference REFERENCE
[--threads THREADS] [--remove-all-dups] [--remove_seq_dups] [--use-gatk-md]
[--strategy STRATEGY] [--keep KEEP]
Options
| Option | Alias | Required | Description |
|---|---|---|---|
-h, --help |
No | Show this help message and exit | |
--sample_id SAMPLE_ID |
-s |
Yes | Sample ID. |
--r1 R1 |
-r1 |
Yes | Path to R1 fastq file. |
--r2 R2 |
-r2 |
Yes | Path to R2 fastq file. |
--out-path OUT_PATH |
-o |
Yes | Output path for the results. |
--reference REFERENCE |
-r |
Yes | Path to the reference genome. |
--threads THREADS |
-t |
No | Number of threads to use. |
--remove-all-dups |
-ra |
No | Remove all duplicates |
--remove_seq_dups |
-rs |
No | Remove sequencing duplicates |
--use-gatk-md |
-ug |
No | Use GATK MarkDuplicatesSpark |
--strategy STRATEGY |
-st |
No | Downsampling strategy |
--keep KEEP |
-k |
No | How much read to keep? Give a ratio |