Usage¶
The RADSex software implements the general command-line interface:
radsex <command> [options]
Available commands
Command |
Description |
|---|---|
depth |
Compute marker depth statistics for each individual |
distrib |
Compute the distribution of markers between compared groups |
freq |
Compute the distribution of markers in all individuals |
map |
Align markers to a genome and compute metrics for each aligned marker |
process |
Compute a table of marker depths from a set of demultiplexed reads files |
signif |
Extract markers significantly associated with phenotypic group from a marker depths table |
subset |
Extract a subset of markers from a marker depths table |
process¶
Generate a table containing the depth of each marker in each individual from the dataset.
Command
radsex process --input-dir input_dir_path --output-file output_file_path [ --threads n_threads --min-depth min_depth ]
Options
Option |
Description |
|---|---|
|
Path to a folder containing demultiplexed reads |
|
Path to the generated marker depths table |
|
Number of threads to use (default: 1) |
|
Minimum depth to consider a marker present in an individual (default: 1) |
Output
#Number of markers : 4
id sequence individual_1 individual_2 individual_3 individual_4 individual_5
0 TGCA..TATT 0 15 24 17 21
1 TGCA..GACC 20 18 3 26 4
2 TGCA..ATCG 2 1 5 16 0
3 TGCA..CCGA 14 29 23 2 19
Note
Input files are automatically dectected from the input directory based on their extensions. Supported extensions are .fa, .fa.gz, .fq, .fq.gz, .fasta, .fasta.gz, .fastq, .fastq.gz, .fna, and .fna.gz. Individual IDs in the output table will be inferred from the input files names after removing the extension. For instance, a file named individual_1.fastq.gz will be attributed the ID individual_1. Make sure to use the same IDs when creating the population map.
distrib¶
Generate a table containing the distribution of markers between two groups of individuals defined in a Group info.
Command
radsex distrib --markers-table markers_table_path --output-file output_file_path --popmap popmap_path [ --min-depth min_depth --groups group1,group2 --signif-threshold signif_threshold --disable-correction ]
Options
Option |
Description |
|---|---|
|
Path to a marker depths table generated by “process” |
|
Path to a tabulated file specifying groups for all individuals |
|
Path to the output file (distribution of markers between groups) |
|
Minimum depth to consider a marker present in an individual |
|
Names of the groups to compare if there are more than two groups in the popmap (–groups group1, group2) |
|
P-value threshold to consider a marker significantly associated with a phenotypic group |
|
If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group |
Output
A Distribution of markers between groups:
Males Females Markers P CorrectedP Signif Bias
0 1 7 1 1 False -0.333
0 2 3 0.39 1 False -0.666
0 3 1 0.10 1 False -1.000
1 0 6 1 1 False 0.333
1 1 5 1 1 False 0.000
1 2 1 1 1 False -0.333
1 3 2 0.39 1 False -0.666
2 0 3 0.39 1 False 0.666
2 1 8 1 1 False 0.333
2 2 4 1 1 False 0.000
2 3 2 1 1 False -0.333
3 0 4 0.10 1 False 1.000
3 1 7 0.39 1 False 0.666
3 2 6 1 1 False 0.333
3 3 9 1 1 False 0.000
signif¶
Find markers significantly associated with groups of individuals defined in a Group info.
Command
radsex signif --markers-table markers_table_path --output-file output_file_path --popmap popmap_path [ --min-depth min_depth --groups group1,group2 --signif-threshold signif_threshold --disable-correction --output-fasta ]
Options
Option |
Description |
|---|---|
|
Path to a marker depths table generated by “process” |
|
Path to a tabulated file specifying groups for all individuals |
|
Path to the output file (distribution of markers between groups) |
|
Minimum depth to consider a marker present in an individual |
|
Names of the groups to compare if there are more than two groups in the popmap (–groups group1, group2) |
|
P-value threshold to consider a marker significantly associated with a phenotypic group |
|
If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group |
|
If set, markers are saved to a fasta file instead of a markers depth table |
Output
#Number of markers : 4
id sequence individual_1 individual_2 individual_3 individual_4 individual_5
0 TGCA..TATT 0 15 24 17 21
1 TGCA..GACC 20 18 3 26 4
2 TGCA..ATCG 2 1 5 16 0
3 TGCA..CCGA 14 29 23 2 19
>4495827_F:0_M:21_p:1.14577e-07_pcorr:2.64584e-03_mindepth:10
TGCAG.....GGATGTGTATCCATA
>4609394_F:0_M:23_p:1.08057e-08_pcorr:3.13548e-04_mindepth:10
TGCAG.....GGTTCCATCCCAAAT
>4661391_F:0_M:26_p:1.92225e-10_pcorr:8.95316e-06_mindepth:10
TGCAG.....GTAGAGTGACCAGTT
>5182569_F:0_M:22_p:3.62243e-08_pcorr:6.43275e-04_mindepth:10
TGCAG.....ACATGCTGTAAATGC
>5625957_F:0_M:25_p:7.91633e-10_pcorr:1.16345e-06_mindepth:10
TGCAG.....CTGGAGAAGAGTAGG
map¶
Align markers to a genome and compute bias and probability of association with group for each aligned marker.
Command
radsex map --input-file input_file_path --output-file output_file_path --population-map popmap_file_path --genome-file genome_file_path [ --min-depth min_depth --min-quality min_quality --min-frequency min_frequency ]
Options
Option |
Description |
|---|---|
|
Path to a marker depths table generated by “process” |
|
Path to a tabulated file specifying groups for all individuals |
|
Path to the output file (distribution of markers between groups) |
|
Path to the genome file |
|
Minimum depth to consider a marker present in an individual |
|
Names of the groups to compare if there are more than two groups in the popmap (–groups group1, group2) |
|
Minimum mapping quality to retain a marker |
|
Minimum frequency of individuals in which a marker is present to retain a marker |
|
P-value threshold to consider a marker significantly associated with a phenotypic group |
|
If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group |
Output
Contig Position Length Marker_id Bias P CorrectedP Signif
LG03 18366992 36623554 4335174 -0.202 0.073 1 False
LG05 28289991 33792114 4335919 0 1 1 False
LG05 29738230 33792114 4336169 0.149 0.356 1 False
LG22 71119 28810691 4336631 0.159 0.162 1 False
LG15 20142338 30000224 4336732 0 1 1 False
LG02 26668964 31118443 4337320 0 1 1 False
LG03 4463700 36623554 4337383 -0.033 0.973 1 False
LG13 32240045 33409148 4338936 -0.073 0.704 1 False
LG13 19113343 33409148 4340342 0.064 0.479 1 False
LG22 22503191 28810691 4341087 -0.080 0.704 1 False
LG01 17881236 39973033 8678129 -0.736 1.112e-03 1 True
LG01 16475480 39973033 8888270 -0.705 4.773e-03 1 True
LG01 15761951 39973033 8954765 -0.769 2.629e-04 1 True
LG01 16562550 39973033 8990122 -0.736 1.112e-03 1 True
subset¶
Extract a subset of markers from a markers depth table based on presence in individuals from each compared group.
Command
radsex subset --markers-table markers_table_path --output-file output_file_path --popmap popmap_path [ --min-depth min_depth --groups group1,group2 --signif-threshold signif_threshold --disable-correction --min-group1 min_group1 --min-group2 min_group2 --max-group1 max_group1 --max-group2 max_group2 --min-individuals min_individuals --max-individuals max_individuals --output-fasta ]
Options
Option |
Description |
|---|---|
|
Path to a marker depths table generated by “process” |
|
Path to a tabulated file specifying groups for all individuals |
|
Path to the output file (subset of markers) |
|
Minimum depth to consider a marker present in an individual |
|
Names of the groups to compare if there are more than two groups in the popmap (–groups group1, group2) |
|
P-value threshold to consider a marker significantly associated with a phenotypic group |
|
If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group |
|
If set, markers are saved to a fasta file instead of a markers depth table |
|
Minimum number of individuals from the first group to retain a marker in the subset |
|
Minimum number of individuals from the second group to retain a marker in the subset |
|
Maximum number of individuals from the first group to retain a marker in the subset |
|
Maximum number of individuals from the second group to retain a marker in the subset |
|
Minimum number of individuals to retain a marker in the subset |
|
Maximum number of individuals to retain a marker in the subset |
Output
#Number of markers : 4
id sequence individual_1 individual_2 individual_3 individual_4 individual_5
0 TGCA..TATT 0 15 24 17 21
1 TGCA..GACC 20 18 3 26 4
2 TGCA..ATCG 2 1 5 16 0
3 TGCA..CCGA 14 29 23 2 19
>4495827_F:0_M:21_p:1.14577e-07_pcorr:2.64584e-03_mindepth:10
TGCAG.....GGATGTGTATCCATA
>4609394_F:0_M:23_p:1.08057e-08_pcorr:3.13548e-04_mindepth:10
TGCAG.....GGTTCCATCCCAAAT
>4661391_F:0_M:26_p:1.92225e-10_pcorr:8.95316e-06_mindepth:10
TGCAG.....GTAGAGTGACCAGTT
>5182569_F:0_M:22_p:3.62243e-08_pcorr:6.43275e-04_mindepth:10
TGCAG.....ACATGCTGTAAATGC
>5625957_F:0_M:25_p:7.91633e-10_pcorr:1.16345e-06_mindepth:10
TGCAG.....CTGGAGAAGAGTAGG
freq¶
Generate a table containing the distribution of markers in the entire dataset.
Command
radsex freq --markers-table markers_table_path --output-file output_file_path [ --min-depth min_depth ]
Options
Option |
Description |
|---|---|
|
Path to a marker depths table generated by “process” |
|
Path to the output file (distribution of markers between groups) |
|
Minimum depth to consider a marker present in an individual |
Output
A Distribution of markers in the population:
Frequency Count
1 10389
2 3869
3 2884
4 1824
5 1672
6 1276
7 1261
8 1278
9 1355
10 1291
depth¶
Compute the number of reads and markers as well as the minimum, maximum, median, and average marker depth in each individual from the dataset.
Command
radsex depth --markers-table markers_table_path --popmap popmap_file --output-file output_file_path
Options
Option |
Description |
|---|---|
|
Path to a marker depths table generated by “process” |
|
Path to a tabulated file specifying groups for all individuals |
|
Path to the output file (distribution of markers between groups) |
|
Minimum depth to consider a marker present in an individual |
Output
A Distribution of marker depth in each individual:
Individual Group Reads Markers Retained Min_depth Max_depth Median_depth Average_depth
SRR1519834 M 3929067 669084 72938 0 60604 60 71
SRR1519837 M 6018684 963531 72938 0 48628 44 53
SRR1519830 F 4844480 818700 72938 0 35358 54 72
SRR1519853 M 3462244 502028 72938 0 27276 28 33
SRR1519824 F 3518348 604081 72938 0 23912 21 27
SRR1519819 F 3815684 622309 72938 0 36001 24 32
SRR1519846 M 4731003 758814 72938 0 30307 31 36
SRR1519829 F 6928277 909117 72938 0 64723 45 61
SRR1519812 F 7547724 1165312 72938 0 44358 36 46
SRR1519862 M 5948867 945346 72938 0 64356 69 81