Misc_Utils

A collection of Bash and Python scripts to perform various small tasks for DNA sequence data.

Contains the following scripts:

• Add_ID_to_VCF.py: Add stable identifiers to the ID field of a VCF.
• Count_Variants_Per_Contig.py: Counts how many variants there are in each contig/chromosome in a VCF
• Filter_VCF.py: Apply arbitrary filters to a VCF file.
• Genotype_Matrix_To_Fasta.py: Convert a genotyping matrix to FASTA for input into libsequence tools. Because it assumes a fixed genotyping platform, it will remove monomorphic markers as well.
• Mass_Job_Deletion.sh: Delete all owned MSI jobs on the current server. Does not ask for confirmation, be careful.
• PLINK_to_NicholsonFST.py: Convert from PLINK file formats to those used as input for an F_ST estimator developed by Nicholson et al. 2002 and implemented in the R package 'popgen'
• Percent_Similarity.py: Calculate average percent similarity for SNPs listed in a VCF file.
• Parallel_ms.py: Splits a big batch of ms simulations over multiple cores to make it run in less walltime.
• Plot_SFS.R: Plot site frequency spectra.
• Remove_Monomorphic.py: Remove monomorphic sites from a FASTA alignment.
• SNP_Effect_Predictor.py: Predicts silent/nonsynonymous SNPs in a VCF, given a GFF and a reference assembly. Requires gff_parse.py and Biopython. SNPEff does this, but SNP_Effect_Predictor.py was written to work with a genome with an incomplete assembly.
• SRA_Fetch.sh: Downloads .sra files from NCBI's Short Read Archive using LFTP. Can fetch based on Experiment number, Run number, Sample number, or Study number.
• Strip_BAM.sh: Trim down a BAM file to just regions of interest. Requires SAMTools.
• VCF_MAF.py: Counts the number of alternate and reference reads in a VCF. Useful only for BWC's BSA project (for now)
• VCF_To_Htable.py: Translates a VCF into a Hudson-like polytable. Chokes on heterozygous sites.
• VCF_from_FASTA_2.py: Report variant sites in a FASTA multiple sequence alignment as a VCF. This was designed for Sanger reads aligned to a genomic locus.
• gff_parse.py: Python classes to try to make reading/fetching chunks of data from a GFF v3 file easier. Gets parent, child, and "sibling" features given a feature identifier.
• ms_FreqFilter.py: Apply a 'discovery panel' to ms output. Used in Fang et al. 2013 in G3 to simulate ascertainment for a genotyping platform.
• transpose.sh: Transpose a matrix.