Commands parameters

Insert single-nucleotide variants

This command inserts single-nucleotide variants (SNVs) in a given fasta file.

python insert_SNVs.py \
    --fasta_input [reference.fa] \
    --fasta_output [output.fa] \
    --freq_file [frequency_file.txt] \
    --chrom [chromosome_name] \
    --vcf_output [output.vcf]

Required arguments:

  --fasta_input [input.fasta]
                       Input fasta file to be used as reference to
                       receive single-nucleotide variants (SNVs).

  --fasta_output [output.fasta]
                       Output fasta file with random SNVs,
                       based in frequencies.

  --freq_file [freq.txt]
                       Text file SNV frequencies.

  --vcf_output [output.vcf]
                       VCF file generated with SNVs inserted.

  --chrom [chromosome]
                       Chromosome name.

Optional arguments:

  -h/--help            
                       Shows the help message and exits

Simulate structural variant regions

python simulate_SV_BED.py \
    --dup_lens [duplication_lengths_file.txt] \
    --del_lens [deletion_lengths_file.txt] \
    --inv_lens [inversion_lengths_file.txt] \
    --bal_trans_lens [balanced_translocations_lengths_file.txt] \
    --unb_trans_lens [unbalanced_translocations_lengths_file.txt] \
    --chroms [chromosomes_range] \
    --chroms_trans [translocated_chromosomes_range] \
    --chrom_lens [chromosome_lengths.txt] \
    --gaps [genome_gaps.txt] \
    -o [output_file.bed]

Required arguments:

  --chrom_lens [chrom_lens.txt]
                       Text file with chromosome lengths.

  --output/-o [output.bed]
                       BED output file.

  --gaps [gaps_file.bed]      
                       BED file with regions to avoid
                       (centromeres and telomeres).

  --chroms [chrom_range]
                       Chromosome names to generate SV regions.
                       (e.g. 3, 1-5, 20-Y)
                       (default: all)

Optional arguments:

  -h, --help            
                        Shows the help message and exits

  --del_lens [del_lens.txt]
                       Text file with deletion
                       lengths (one per line).

  --dup_lens [dup_lens.txt]
                       Text file with duplication
                       lengths (one per line).

  --inv_lens [inv_lens.txt]
                       Text file with inversion
                       lengths (one per line).

  --bal_trans_lens [bal_lens.txt]
                       Text file with balanced translocation
                       lengths (one per line).

  --unb_trans_lens [unb_lens.txt]
                       Text file with unbalanced translocation
                       lengths (one per line).

  --chroms_trans [chrom_range]
                       Chromosomes from which translocations
                       will come from (e.g. 3, 1-5, 20-Y)
                       (default: all)

  --distance/-d [distance between SVs]
                       Average distance between SVs in a
                       countinuous (ungapped) region.
                       (default: 100000)

  --dist_sd/-sd [distance st. dev.]
                       Standard deviation of distance between
                       SVs in a countinuous (ungapped) region.
                       (default: 10000)

  -v/--verbose
                       Shows more details about program execution.

Insert structural variants

python insert_SVs.py \
    -i [input.fa] \
    -o [output.fa] \
    --chrom_lens [chromosome_lengths.txt] \
    --chrom [chromosome_name] \
    --bed [SVs.bed] \
    -v

Required arguments:

 --fasta_input [input.fasta]
                       Input fasta file to be used as reference to
                       receive structural variants (SVs).

 --fasta_output [output.fasta]
                       Output fasta file with SVs,
                       based on BED file.

 --chrom_lens [chrom_lens.txt]
                       Text file with chromosome lengths.

 --bed [SVs.bed]
                       BED file with SVs to be inserted
                       (it can be provided by user, or just
                       the output of 'simulate_SV_BED.py').

Optional arguments:

 --fasta_label [fasta_label]
                       Name to label fasta sequences.

 -h/--help            
                       Shows the help message and exits.

 -v/--verbose
                       Shows more details about program execution.

Create reads

Example with paired-end reads:

python create_reads.py \
    -pe \
    -i [input.fa] \
    -o [output.fq] \
    --cov [coverage] \
    --read_len [read_length] \
    --snp_rate [SNP_rate_for_reads] \
    --del_rate [deletion_rate_for_reads] \
    --ins_rate [insertion_rate_for_reads] \
    --read_label [label_for_reads] \
    -v

Required arguments:

 --fasta_input/-i [input.fasta]
                       Fasta file to be changed with SVs.

 --output_file/-o [output.fq]
                       Output file for reads. It must finish with
                       .fq/.fastq (paired-end option will automatically
                       change file names to output1.fq and output2.fq).

 --cov [coverage]      
                       Average coverage.

 --read_len [avg read len]
                       Average read length (this length will be fix
                       for short reads, but not for long reads).
                       This parameters will determine whether to
                       create reads according to Illumina error rate
                       (length <= 500) or PacBio error rate (length > 500).

Optional arguments:

 -h/--help            
                       Shows the help message and exits.

 -pe                   
                       Add option to generate paired-end reads.
                       If not given, single-end reads will be
                       generated.

 --ins_rate [insertion rate]
                       Insertion error rate for reads.
                       (default: 0.12)

 --del_rate [deletion rate]
                       Deletion error rate for reads.
                       (default: 0.02)                          
 --snp_rate [snp rate]
                       SNP error rate for reads.
                       (default: 0.01)

 --insert_size [insert size]
                       Insert size for short reads.
                       (default: 300)                           
 --insert_sd [insert st. dev.]
                       Insert standard deviation for short reads.
                       (default: 50)

 --alpha [alpha value]
                       Alpha value for beta distribution of base qualities.
                       (default: 2)

 --beta [beta value]           
                       Beta for beta distribution of read lengths.
                       (default: 10)

  --read_label [label]
                        Label to add in each read.

  -v/--verbose
                       Shows more details about program execution.

Commands parameters

Table of Contents

Download databases

Insert single-nucleotide variants

Simulate structural variant regions

Insert structural variants

Create reads