Last update: 1372 goats - November 9th 2020. Data access (authentification required): Shared Data.

1. The Genome directory contains:
• genome FASTA file (29 chromosomes + MT + 29 877 scaffolds = 29 907 sequences)
• DICT file
• tab-delimited text file (chromosome_name, length) sorted by length.
2. The BQSR directory contains the VCF file used to GATK base recalibration
3. The VQSR directory contains all the VCF files used to GATK variant recalibration (see README for details)
4. The Vargoats_1159_20201109 directory contains:
• VCF file for indels (VQSR filtered) - 13 607 850 indels
• VCF file for snps (VQSR filtered) - 114 244 623 snps
• 30 splitted by chromosome VCF files (VQSR + GATK QUAL>100 + countVariant()>=2 + biallelic) - 74 274 427 snps
• MD5 file to check the integrity of the download process.
5. The Vargoats_1159_20201109_filtered_20210201 directory contains:
• 30 splitted by chromosome VCF files (see README for filtering parameters) - 26 751 539 snps
• MD5 file to check the integrity of the download process.
6. The Vargoats_1372_20201008 directory contains:
• VCF file for indels (VQSR filtered) - 13 820 197 indels
• 30 splitted by chromosome VCF files (VQSR + GATK QUAL>100 + countVariant()>=2 + biallelic) - 77 280 295 snps
• MD5 file to check the integrity of the download process.
7. The Vargoats_1372_20201008_filtered_20210716 directory contains:
• 30 splitted by chromosome VCF files (see README for filtering parameters) - 28 645 747 snps
• MD5 file to check the integrity of the download process.
8. The Vargoats_1372_20201008_filtered_phasedBeagle5.3 directory contains:
• 29 splitted by chromosome VCF files - Haplotype phasing performed with Beagle 5.3
• beagle5.3_phasing_summary text file.
9. The Vargoats_1372_20230313 directory contains the same VCF of the Vargoats_1372_20201008 directory but reannotated by snfEff (version 5.1) against ARS1.105
10. Note: For Vargoats_1372_20201008... directories, the VCF annotation have been done using snpEff (version 4.3t) and the NCBI Capra hircus annotation release 102.