Various scripts for filtering and manipulating vcf files for genomic analyses. All scripts require PyVCF; additional modules required listed where applicable.
find_chrom.py Using BLASTn output (as an .xml), find loci mapped to a specific locus (user-specified) and create an output file excluding them. Initially written to remove Z-linked loci from UCE datasets. Requirements: BioPython, phyluce
biallelicSNPs.py Find non-biallelic SNPs and create a new vcf file without them. Necessary for preparing files for analyses limited to biallelic data.
randomSNP.py When thinning to 1 SNP per locus, select a random SNP (rather than just the first SNP listed).