removed unnecessary files, updated usage.md

docs/Usage.md

@@ -86,6 +86,150 @@ python PATH_TO_NANOCALLER_REPOSITORY/scripts/NanoCaller_WGS.py
 ## General Usage Options
 
 ### Single Chromosome Variant Calling
+```
+usage: NanoCaller.py [-h] [-mode MODE] [-seq SEQUENCING] [-cpu CPU]
+                     [-mincov MINCOV] [-maxcov MAXCOV] [-keep_bam] [-o OUTPUT]
+                     [-prefix PREFIX] [-sample SAMPLE]
+                     [-include_bed INCLUDE_BED] [-exclude_bed EXCLUDE_BED]
+                     [-start START] [-end END] [-p PRESET] -bam BAM -ref REF
+                     -chrom CHROM [-snp_model SNP_MODEL]
+                     [-min_allele_freq MIN_ALLELE_FREQ]
+                     [-min_nbr_sites MIN_NBR_SITES]
+                     [-nbr_t NEIGHBOR_THRESHOLD] [-sup]
+                     [-indel_model INDEL_MODEL] [-ins_t INS_THRESHOLD]
+                     [-del_t DEL_THRESHOLD] [-win_size WIN_SIZE]
+                     [-small_win_size SMALL_WIN_SIZE] [-phase_bam]
+                     [-enable_whatshap]
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Required Arguments:
+  -bam BAM, --bam BAM   Bam file, should be phased if 'indel' mode is selected
+                        (default: None)
+  -ref REF, --ref REF   Reference genome file with .fai index (default: None)
+  -chrom CHROM, --chrom CHROM
+                        Chromosome (default: None)
+
+Preset:
+  -p PRESET, --preset PRESET
+                        Apply recommended preset values for SNP and Indel
+                        calling parameters, options are 'ont', 'ul_ont',
+                        'ul_ont_extreme', 'ccs' and 'clr'. 'ont' works well
+                        for any type of ONT sequencing datasets. However, use
+                        'ul_ont' if you have several ultra-long ONT reads up
+                        to 100kbp long, and 'ul_ont_extreme' if you have
+                        several ultra-long ONT reads up to 300kbp long. For
+                        PacBio CCS (HiFi) and CLR reads, use 'ccs'and 'clr'
+                        respectively. Presets are described in detail here: gi
+                        thub.com/WGLab/NanoCaller/blob/master/docs/Usage.md#pr
+                        eset-options. (default: None)
+
+Configurations:
+  -mode MODE, --mode MODE
+                        NanoCaller mode to run, options are 'snps',
+                        'snps_unphased', 'indels' and 'both'. 'snps_unphased'
+                        mode quits NanoCaller without using WhatsHap for
+                        phasing. (default: both)
+  -seq SEQUENCING, --sequencing SEQUENCING
+                        Sequencing type, options are 'ont', 'ul_ont',
+                        'ul_ont_extreme', and 'pacbio'. 'ont' works well for
+                        any type of ONT sequencing datasets. However, use
+                        'ul_ont' if you have several ultra-long ONT reads up
+                        to 100kbp long, and 'ul_ont_extreme' if you have
+                        several ultra-long ONT reads up to 300kbp long. For
+                        PacBio CCS (HiFi) and CLR reads, use 'pacbio'.
+                        (default: ont)
+  -cpu CPU, --cpu CPU   Number of CPUs to use (default: 1)
+  -mincov MINCOV, --mincov MINCOV
+                        Minimum coverage to call a variant (default: 8)
+  -maxcov MAXCOV, --maxcov MAXCOV
+                        Maximum coverage of reads to use. If sequencing depth
+                        at a candidate site exceeds maxcov then reads are
+                        downsampled. (default: 160)
+
+Variant Calling Regions:
+  -include_bed INCLUDE_BED, --include_bed INCLUDE_BED
+                        Only call variants inside the intervals specified in
+                        the bgzipped and tabix indexed BED file. If any other
+                        flags are used to specify a region, intersect the
+                        region with intervals in the BED file, e.g. if -chom
+                        chr1 -start 10000000 -end 20000000 flags are set, call
+                        variants inside the intervals specified by the BED
+                        file that overlap with chr1:10000000-20000000. Same
+                        goes for the case when whole genome variant calling
+                        flag is set. (default: None)
+  -exclude_bed EXCLUDE_BED, --exclude_bed EXCLUDE_BED
+                        Path to bgzipped and tabix indexed BED file containing
+                        intervals to ignore for variant calling. BED files of
+                        centromere and telomere regions for the following
+                        genomes are included in NanoCaller: hg38, hg19, mm10
+                        and mm39. To use these BED files use one of the
+                        following options: ['hg38', 'hg19', 'mm10', 'mm39'].
+                        (default: None)
+  -start START, --start START
+                        start, default is 1 (default: None)
+  -end END, --end END   end, default is the end of contig (default: None)
+
+SNP Calling:
+  -snp_model SNP_MODEL, --snp_model SNP_MODEL
+                        NanoCaller SNP model to be used (default: ONT-HG002)
+  -min_allele_freq MIN_ALLELE_FREQ, --min_allele_freq MIN_ALLELE_FREQ
+                        minimum alternative allele frequency (default: 0.15)
+  -min_nbr_sites MIN_NBR_SITES, --min_nbr_sites MIN_NBR_SITES
+                        minimum number of nbr sites (default: 1)
+  -nbr_t NEIGHBOR_THRESHOLD, --neighbor_threshold NEIGHBOR_THRESHOLD
+                        SNP neighboring site thresholds with lower and upper
+                        bounds seperated by comma, for Nanopore reads
+                        '0.4,0.6' is recommended, for PacBio CCS anc CLR reads
+                        '0.3,0.7' and '0.3,0.6' are recommended respectively
+                        (default: 0.4,0.6)
+  -sup, --supplementary
+                        Use supplementary reads (default: False)
+
+Indel Calling:
+  -indel_model INDEL_MODEL, --indel_model INDEL_MODEL
+                        NanoCaller indel model to be used (default: ONT-HG002)
+  -ins_t INS_THRESHOLD, --ins_threshold INS_THRESHOLD
+                        Insertion Threshold (default: 0.4)
+  -del_t DEL_THRESHOLD, --del_threshold DEL_THRESHOLD
+                        Deletion Threshold (default: 0.6)
+  -win_size WIN_SIZE, --win_size WIN_SIZE
+                        Size of the sliding window in which the number of
+                        indels is counted to determine indel candidate site.
+                        Only indels longer than 2bp are counted in this
+                        window. Larger window size can increase recall, but
+                        use a maximum of 50 only (default: 40)
+  -small_win_size SMALL_WIN_SIZE, --small_win_size SMALL_WIN_SIZE
+                        Size of the sliding window in which indel frequency is
+                        determined for small indels (default: 4)
+
+Output Options:
+  -keep_bam, --keep_bam
+                        Keep phased bam files. (default: False)
+  -o OUTPUT, --output OUTPUT
+                        VCF output path, default is current working directory
+                        (default: None)
+  -prefix PREFIX, --prefix PREFIX
+                        VCF file prefix (default: variant_calls)
+  -sample SAMPLE, --sample SAMPLE
+                        VCF file sample name (default: SAMPLE)
+
+Phasing:
+  -phase_bam, --phase_bam
+                        Phase bam files if snps mode is selected. This will
+                        phase bam file without indel calling. (default: False)
+  -enable_whatshap, --enable_whatshap
+                        Allow WhatsHap to change SNP genotypes when phasing
+                        using --distrust-genotypes and --include-homozygous
+                        flags (this is not the same as regenotyping),
+                        considerably increasing the time needed for phasing.
+                        It has a negligible effect on SNP calling accuracy for
+                        Nanopore reads, but may make a small improvement for
+                        PacBio reads. By default WhatsHap will only phase SNP
+                        calls produced by NanoCaller, but not change their
+                        genotypes. (default: False)
+```
 
 ### Whole Genome Variant Calling
 ```
@@ -116,7 +260,15 @@ Preset:
   -p PRESET, --preset PRESET
                         Apply recommended preset values for SNP and Indel
                         calling parameters, options are 'ont', 'ul_ont',
-                        'ul_ont_extreme', 'ccs' and 'clr' (default: None)
+                        'ul_ont_extreme', 'ccs' and 'clr'. 'ont' works well
+                        for any type of ONT sequencing datasets. However, use
+                        'ul_ont' if you have several ultra-long ONT reads up
+                        to 100kbp long, and 'ul_ont_extreme' if you have
+                        several ultra-long ONT reads up to 300kbp long. For
+                        PacBio CCS (HiFi) and CLR reads, use 'ccs'and 'clr'
+                        respectively. Presets are described in detail here: gi
+                        thub.com/WGLab/NanoCaller/blob/master/docs/Usage.md#pr
+                        eset-options. (default: None)
 
 Configurations:
   -mode MODE, --mode MODE
@@ -126,7 +278,13 @@ Configurations:
                         phasing. (default: both)
   -seq SEQUENCING, --sequencing SEQUENCING
                         Sequencing type, options are 'ont', 'ul_ont',
-                        'ul_ont_extreme', and 'pacbio' (default: ont)
+                        'ul_ont_extreme', and 'pacbio'. 'ont' works well for
+                        any type of ONT sequencing datasets. However, use
+                        'ul_ont' if you have several ultra-long ONT reads up
+                        to 100kbp long, and 'ul_ont_extreme' if you have
+                        several ultra-long ONT reads up to 300kbp long. For
+                        PacBio CCS (HiFi) and CLR reads, use 'pacbio'.
+                        (default: ont)
   -cpu CPU, --cpu CPU   Number of CPUs to use (default: 1)
   -mincov MINCOV, --mincov MINCOV
                         Minimum coverage to call a variant (default: 8)
@@ -280,7 +438,7 @@ Preset `ccs` is equivalent to:
 --indel_model CCS-HG002
 --neighbor_threshold '0.3,0.7'
 --ins_threshold 0.4
---del_threshold
+--del_threshold 0.4
 --enable_whatshap
 ```