Fixed a bug in the vcf2hdf5_parallel script (#58 - @travc). Fixed a bug relating to the is_snp field (#60 - @podpearson). Removed numpy as a build dependency (#46). Increased the default dtype size for the EFF Amino_Acid_Change field (#62 - @travc). Ensure vcflib doesn't call system exit(1) but raises exceptions instead (#48). Added --compress option to vcf2npy script to support saving to .npz files instead of .npy (#59). Added support for new calldata fields genotype_ac and ploidy to provide support for VCF files with variable ploidy (#63)
This file is the output of the pyRAD pipeline (VCF format) ran on the raw sequence reads (accessible...
R script for converting 'vcf' data from SNP pipeline to a single datafile of genotype and read count...
This is a .vcf file produced by calling variant genetic sites using samtools and bcftools. For each ...
Summary of new changes: I fixed multiple bugs that resulted from lack of coverage of some possible i...
Bug fixed, improved phasing, and PofO assignment for variants with 1/2 genotype. Making SNVs as defa...
VCF file containing info for SNPs called using the getsnpsfrommpileup.pl script. Settings used were:...
Changes Add support for input directly VCF (--vcf) files instead of FASTA or FASTQ files. These VCF...
Added p14ARF as a canonical isoform for CDKN2A, in addition to p16INK4A. vcf2vcf can now run mpileup...
Fix issues when ALT alleles are a SNP and indel, both non-REF When looking up known variants, match ...
This file is a vcf file containing the SNP calls at the eight SNPs identified as outliers. Seven of ...
SUMMARY: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as...
Summary: The Variant Call Format (VCF) is a generic format for storing DNA polymorphism data such as...
<div><div><div>SNP calls in VCF format. As used in for:</div><div><br></div><div>Jeffares DC et al (...
Changes Fixes #26 and #41 by annotating VCFs with homoplasmic problematic sites from DeMaio. These ...
v.0.3.6 fixed a bug in vcf_imputation, the function now calls genomic_converter with all the bell...
This file is the output of the pyRAD pipeline (VCF format) ran on the raw sequence reads (accessible...
R script for converting 'vcf' data from SNP pipeline to a single datafile of genotype and read count...
This is a .vcf file produced by calling variant genetic sites using samtools and bcftools. For each ...
Summary of new changes: I fixed multiple bugs that resulted from lack of coverage of some possible i...
Bug fixed, improved phasing, and PofO assignment for variants with 1/2 genotype. Making SNVs as defa...
VCF file containing info for SNPs called using the getsnpsfrommpileup.pl script. Settings used were:...
Changes Add support for input directly VCF (--vcf) files instead of FASTA or FASTQ files. These VCF...
Added p14ARF as a canonical isoform for CDKN2A, in addition to p16INK4A. vcf2vcf can now run mpileup...
Fix issues when ALT alleles are a SNP and indel, both non-REF When looking up known variants, match ...
This file is a vcf file containing the SNP calls at the eight SNPs identified as outliers. Seven of ...
SUMMARY: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as...
Summary: The Variant Call Format (VCF) is a generic format for storing DNA polymorphism data such as...
<div><div><div>SNP calls in VCF format. As used in for:</div><div><br></div><div>Jeffares DC et al (...
Changes Fixes #26 and #41 by annotating VCFs with homoplasmic problematic sites from DeMaio. These ...
v.0.3.6 fixed a bug in vcf_imputation, the function now calls genomic_converter with all the bell...
This file is the output of the pyRAD pipeline (VCF format) ran on the raw sequence reads (accessible...
R script for converting 'vcf' data from SNP pipeline to a single datafile of genotype and read count...
This is a .vcf file produced by calling variant genetic sites using samtools and bcftools. For each ...