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help.txt
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help.txt
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usage: isafe [-h] [-v] [--format FORMAT] --input INPUT --output OUTPUT [--vcf-cont VCF_CONT] [--sample-case SAMPLE_CASE]
[--sample-cont SAMPLE_CONT] [--AA AA] [--region REGION] [--MaxRegionSize MAXREGIONSIZE]
[--MinRegionSize-bp MINREGIONSIZE_BP] [--MinRegionSize-ps MINREGIONSIZE_PS] [--MaxGapSize MAXGAPSIZE]
[--window WINDOW] [--step STEP] [--topk TOPK] [--MaxRank MAXRANK] [--MaxFreq MAXFREQ]
[--RandomSampleRate RANDOMSAMPLERATE] [--ForceRandomSample] [--IgnoreGaps] [--StatusOff] [--WarningOff]
[--OutputPsi] [--SAFE]
====================================================================
iSAFE: (i)ntegrated (S)election of (A)llele (F)avored by (E)volution
====================================================================
Source code & further instructions can be found at: https://github.com/alek0991/iSAFE
iSAFE v1.1.1
--------------------------------------------------------------------
options:
-h, --help show this help message and exit
-v, --version show program's version number and exit
--format FORMAT, -f FORMAT
<string>: Input format. <FORMAT> must be either hap or vcf (see the manual for more details).
iSAFE can handle two types of inputs (phased haplotypes are required):
* vcf format: --format vcf or -f vcf
- vcf format only accepts indexed bgzipped VCF (vcf.gz with index file) or indexed bcf files (.bcf with index file).
- When input format is vcf, Ancestral Allele file (--AA) must be given.
* hap format: --format hap or -f hap
- Input with hap format is not allowed with any of these: --vcf-cont, --sample-case, --sample-cont, --AA.
- With hap format, iSAFE assumes that derived allele is 1 and ancestral allele is 0 in the input file,
and the selection is ongoing (the favored mutation is not fixed).
Default: vcf
--input INPUT, -i INPUT
<string>: Path to the input (case population).
* Input positions must be sorted numerically, in increasing order.
--output OUTPUT, -o OUTPUT
<string>: Path to the output(s).
* iSAFE generates <OUTPUT>.iSAFE.out
* When --OutputPsi is set, iSAFE generates <OUTPUT>.Psi.out in addition to <OUTPUT>.iSAFE.out
--vcf-cont VCF_CONT <string>: Path to the phased control population.
* only accepts indexed bgzipped VCF (vcf.gz with index file) or indexed bcf files (.bcf with index file).
* This is optional but recommended for capturing fixed sweeps.
* This option is only available with --format vcf.
* You can choose a subset of samples in this file by using --sample-cont option,
otherwise all the samples in this file are cosidered as control population.
* You must use --sample-case and --sample-cont when --input and --vcf-cont are the same (all samples are provided in a single vcf file).
* You can (you don't have to) use 1000 Genome Project populations as control.
- Download link of phased VCF files of 1000GP (GRCh37/hg19): http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
- Download link of phased VCF files of 1000GP (GRCh38/hg38): http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/
--sample-case SAMPLE_CASE
<string>: Path to the file containing sample ID's of the case population.
* This option is only available in --format vcf.
* When this option is not used all the samples in the --input are considered as the case samples.
* This file must have two columns, the first one is population and the second column
is sample ID's (must be a subset of ID's used in the --input vcf file).
* This file must be TAB separated, no header, and comments by #.
* You must use --sample-case and --sample-cont when --input and --vcf-cont are the same (all samples are provided in a single vcf file).
* Population column (first column) can have more than one population name. They are all considered the case populations.
* Sample ID's must be subset of the --input vcf file
--sample-cont SAMPLE_CONT
<string>: Path to the file containing sample ID's of the control population(s).
* This option is only available in --format vcf.
* When this option is not used all the samples in the --vcf-cont are considered as the control samples.
* This file must have two columns, the first one is population and the second column
is sample ID's (must be a subset of ID's used in the --vcf-cont file).
* This file must be TAB separated, no header, and comments by #.
* You must use --sample-case and --sample-cont when --input and --vcf-cont are the same (all samples are provided in a single vcf file).
* Population column (first column) can have more than one population name. They are all considered the control populations.
* Sample ID's must be subset of the --vcf-cont file
--AA AA <string>: Path to the Ancestral Allele (AA) file in FASTA (.fa) format.
* This is strongly recommended in --format vcf. However, if the ancestral allele file is not available the program raises a warning and assumes reference allele (REF) is ancestral allele.
* Download link (GRCh37/hg19): http://ftp.ensembl.org/pub/release-75/fasta/ancestral_alleles/
* Download link (GRCh38/hg38): http://ftp.ensemblorg.ebi.ac.uk/pub/release-88/fasta/ancestral_alleles/
--region REGION <chr:string>:<start position:int>-<end position:int>, the coordinates of the target region in the genome.
* This is required in --format vcf but optional in the --format hap.
* In vcf format, <chr> style (e.g. chr2 or 2) must be consistent with vcf files.
* The <chr> is dumped in --format hap.
* Valid Examples:
2:10000000-15000000
chr2:10000000-15000000
2:10,000,000-15,000,000
chr2:10,000,000-15,000,000
--MaxRegionSize MAXREGIONSIZE
<int>: Maximum region size in bp.
* Consider the memory (RAM) size when change this parameter.
Default: 6000000
--MinRegionSize-bp MINREGIONSIZE_BP
<int>: Minimum region size in bp.
Default: 200000
--MinRegionSize-ps MINREGIONSIZE_PS
<int>: Minimum region size in polymorphic sites.
* Note that --window cannot be smaller than --MinRegionSize-ps.
Default: 1000
--MaxGapSize MAXGAPSIZE
<int>: Maximum gap size in bp.
* When there is a gap larger than --MaxGapSize the program raise an error.
* You can ignore this by setting the --IgnoreGaps flag.
Default: 10000
--window WINDOW <int>: Sliding window size in polymorphic sites.
Default: 300
--step STEP <int>: Step size of sliding window in polymorphic sites.
Default: 150
--topk TOPK <int>: Rank of SNPs used for learning window weights (alpha).
Default: 1
--MaxRank MAXRANK <int>: Ignore SNPs with rank higher than MAXRANK.
* For considering all SNPs set --MaxRank > --window.
* The higher the --MaxRank, the higher the computation time.
Default: 15
--MaxFreq MAXFREQ <float>: Ignore SNPs with frequency higher than MaxFreq.
Default: 0.95
--RandomSampleRate RANDOMSAMPLERATE
<float>: Portion of added random samples.
* RandomSampleRate = RandomSamples/(RandomSamples+CaseSamples).
* Must be non-negative and less than 1.
Default: 0.1
* Ignored when --vcf-case is not used.
* Ignored when MDDAF criterion doesn't recommend adding random samples. The option --ForceRandomSample
can be used to override MDDAF criterion.
--ForceRandomSample, -FRS
<bool>: Set this flag to force the iSAFE to use random samples even when MDDAF doesn't recommend.
* --vcf-cont must be provided.
Default: false
--IgnoreGaps, -IG <bool>: Set this flag to ignore gaps.
Default: false
--StatusOff, -SO <bool>: Set this flag to turn off printing status.
Default: false
--WarningOff, -WO <bool>: Set this flag to turn off warnings.
Default: false
--OutputPsi, -Psi <bool>: Set this flag to output Psi_1 in a text file with suffix .Psi.out.
Default: false
--SAFE <bool>: Set this flag to report the SAFE score of the entire region.
* When the region size is less than --MinRegionSize-ps (Default: 1000 SNPs) or --MinRegionSize-bp (Default: 200kbp),
the region is too small for iSAFE analysis. Therefore, It's better to use --SAFE flag to report the SAFE scores of
the entire region instead of iSAFE scores.
Default: false