IBDGem v2.0.3

Fixed bugs in v2.0.2, specifically issues with parsing genotypes from VCF-formatted input and printing results to output files.

IBDGem v2.0.2

IBD1 likelihoods can now be calculated under LD, in addition to IBD0 (via --LD option). For IBD1 in LD mode, however, the genotypes for the reference and target individuals must be phased (refer to README for details).

IBDGem v2.0.1

Added helper Python and Bash scripts to bin. See updated README under Auxiliary files for description and usage.

IBDGem v2.0

• Added --LD option to account for linkage disequilibrium in IBD0 likelihood calculation using a set of reference samples from the genotype input, which can be specified via --background-list
• Removed aggregate.c module (IBDGem now automatically outputs aggregated likelihoods to a summary file, with the number of SNPs per genomic segment determined via --window-size when running the main program)
• Removed --threads due to negligible performance increase

IBDGem v1.1

• VCF input compatibility (through option --vcf/-V)
• Added --min-qual/-q option to filter sites by value in the QUAL field for VCF files