scripts

Various scripts

Content

vcf_assign_maf_bins.py

Assigns MAF bin to each record from input VCF/BCF file. Requires python 3 and pysam library. Type python vcf_assign_maf_bins.py --help to get the description of all parameters. You can also pipe input/ouput files from/into standard input/output by specifying - instead of file names.

vcf_assign_af_bins.py

Same as vcf_assign_maf_bins.py, but assigns AF bins.

vcf_extract_lof.py

Extracts all Loss-of-Function (LoF) variants from VCF/BCF file annotated using VEP. Requires python 3 and pysam library. Type python vcf_extract_lof.py --help to get the description of all parameters.

vcf_add_cadd_scores.py

Annotates VCF file with CADD scores from https://cadd.gs.washington.edu/download. Note: you must download also the corresponding index files. Type python vcf_add_cadd_scores.py --help to get the description of all parameters.

vcf_assign_depth_bins.py

Assigns AD (allele depth) and DP (total depth) bin to each record from input single sample VCF/BCF file. Requires python 3 and pysam library. Type python vcf_assign_depth_bins.py --help to get the description of all parameters. You can also pipe input/ouput files from/into standard input/output by specifying - instead of file names.

vcf_lof_downsample.py

Subsets random sample from the specified VCF/BCF file and counts number of putative Loss-of-Function variants in the sample. Requires python 3 and pysam library. Requires VCF/BCF file annotated using VEP+LOFTEE. Type python vcf_lof_downsample.py --help to get the description of all parameters.

gencode_cds.py

Extracts CDS (coding sequence regions) for each protein coding gene from GENCODE GTF file. For each gene, it uses a union of CDS regions from all protein coding transcripts. Requires python 3 and intervaltree library. Type python gencode_cds.py --help to get the description of all parameters.

gencode_utr.py

Extracts 5' UTR and 3' UTR regions for each protein coding gene from GENCODE GTF file. For each gene, it uses a union of UTR regions from all protein coding transcripts. Requires python 3 and intervaltree library. Type python gencode_utr.py --help to get the description of all parameters.

bed_compute_gc.py

Computes number of bases (A, C, G, T) and GC-content for regions in BED file. Requires python 3 and pysam library. Type python bed_compute_gc.py --help to get the description of all parameters.

mendelian_per_trio.py

For each variant within trio (mother, father, offspring) identifies possible Mendelian error. Requires python 3 and pysam library. Trios (or nuclear families) must be provided in PED file format (no header). Genotypes for all samples from trios (or nuclear families) must be in the same VCF/BCF file (multiple VCFs/BCFs split by chromosome are allowed). Type mendelian_per_trio.py --help to get the description of all parameters.

mendelian_per_trio_split.py

Same as mendelian_per_trio.py, but requires three sigle-sample input VCF/BCF files: for father, for mother, and for child. Type mendelian_per_trio_split.py --help to get the description of all parameters.

vcf_gene_set.py

Create gene sets file from the VEP annotated VCF/BCF for gene-burden association tests (e.g. using SAIGE or EPACTS). Requires python 3 and pysam library. Type vcf_gene_set.py --help to get the description of all parameters.

variants_per_individual.py

Counts number of variants per individual from VCF/BCF file. Variants are grouped by most severe consequence based on VEP annotations. Requires python 3 and pysam library. Type variants_per_individual.py --help to get the description of all parameters.

plink2reference.py

Helps to align A1/A2 alleles in PLINK to the human genome reference. Keeps only SNPs with A,C,G, and T alleles. Removes palindromic, A/T and G/C, SNPs. Flips everything on the + strand. Type plink2reference.py --help to get the description of all parameters.

plink_dupvar_prioritize.py

Helps to remove duplicated variants with the highest missigness from PLINK files. Type plink_dupvar_prioritize.py --help to get the description of all parameters.

plink_freq_concordance.py

Compares genotype (allele) frequency between two PLINK files using Fisher's exact test. Type plink_freq_concordance.py --help to get the description of all parameters. You may need to load R (use module spider r and module load r) before running the script.

plink_freq_strat_concordance.py

Similar to plink_freq_concordance.py, but allows stratification by the groups (e.g. ancestry). Type plink_freq_strat_concordance.py --help to get the description of all parameters. You may need to load R (use module spider r and module load r) before running the script.

Mahalanobis.py

Performs a Mahalanobis distance of projected genomes. Type Mahalanobis.py --help to get the description of all parameters. Produces for each study sample: distance and its derived p-value per reference categories, and a list of non-rejected reference categories (at input threshold).

merge_minimac_dosages.py

Merges imputed dosages when the genotype imputation was performed in subsets of samples. Subsets can have shared samples. Type merge_minimac_dosages.py --help to get the description of all parameters.

imputation_dosage_comparison.py

Produce sum of absolute differences of Dosages in overlap samples of two impute VCF file (per samples and per variant). Requires python 3, pysam, 'numpy' library.

plink_freq_vs_topmed.py

Compares allele frequencies in PLINK file to TOPMed reference panel. Type plink_freq_vs_topmed.py --help to get the description of all parameters, and look inside the script for the additional hints.

{GRAPH}_Manhattan_Miami.py

Plots a Miami or Manahttan plot (depending on options selected) form Regenie Output.

{GRAPH}_Plot_PCA_Ancestry.py

Plots PCA Projections.