Fast and Memory-Efficient Manipulation and Conversion of VCF
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Documentation for package ‘VCFArrow’ version 0.9.0
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| assess_vcf_coverage | assess_vcf_coverage |
| assess_vcf_missing_data | assess_vcf_missing_data |
| read_vcf | read_vcf |
| set_vcf_groups | set_vcf_groups |
| show-method | Show method for VCFArrow |
| vcf2admixture | vcf2admixture |
| vcf2apparent | vcf2apparent |
| vcf2arlequin | vcf2arlequin |
| vcf2bayesass | vcf2bayesass |
| vcf2bayescan | vcf2bayescan |
| vcf2eigenstrat | vcf2eigenstrat |
| vcf2fasta | vcf2fasta |
| vcf2fineradstructure | vcf2fineradstructure |
| vcf2genepop | vcf2genepop |
| vcf2genlight | vcf2genlight |
| vcf2gt_long | vcf2gt_long |
| vcf2migrate | vcf2migrate |
| vcf2nexus | vcf2nexus |
| vcf2plink_bed | vcf2plink_bed |
| vcf2plink_ped | vcf2plink_ped |
| vcf2related | vcf2related |
| vcf2smartsnp | vcf2smartsnp |
| vcf2snapp | vcf2snapp |
| vcf2snmf | vcf2snmf |
| vcf2structure | vcf2structure |
| vcf2treemix | vcf2treemix |
| VCFArrow-class | VCFArrow S4 class |
| vcf_bind | vcf_bind |
| vcf_copy | vcf_copy |
| vcf_extract_groups | vcf_extract_groups |
| vcf_extract_samples | vcf_extract_samples |
| vcf_filter_adr | vcf_filter_adr |
| vcf_filter_biallelic | vcf_filter_biallelic |
| vcf_filter_coverage | vcf_filter_coverage |
| vcf_filter_hets | vcf_filter_hets |
| vcf_filter_indels | vcf_filter_indels |
| vcf_filter_invariant | vcf_filter_invariant |
| vcf_filter_maf | vcf_filter_maf |
| vcf_filter_missing | vcf_filter_missing |
| vcf_filter_missingness | vcf_filter_missingness |
| vcf_filter_multiSNV | vcf_filter_multiSNV |
| vcf_filter_oneSNV | vcf_filter_oneSNV |
| vcf_filter_paralogs | vcf_filter_paralogs |
| vcf_filter_pass | vcf_filter_pass |
| vcf_filter_quality | vcf_filter_quality |
| vcf_filter_rank | vcf_filter_rank |
| vcf_filter_rpt | vcf_filter_rpt |
| vcf_gc | Garbage-collect VCFArrow temp directories |
| vcf_memory_estimate | Estimate RAM required for a VCFArrow export operation |
| vcf_set_workers | vcf_set_workers |
| vcf_stats | vcf_stats |
| vcf_sub_SNVs | vcf_sub_loci |
| vcf_sub_SNVs_stratified | vcf_sub_loci_stratified |
| vcf_suggest_chunk_size | Suggest a chunk_size for read_vcf() given available RAM |
| vcf_theta | vcf_theta |
| write_vcf | write_vcf |
| [-method | Subset method for VCFArrow |