Published June 20, 2022
| Version 1.1.0
Dataset
Open
PRJEB16533 raw variants
Creators
- 1. University of the Basque Country
- 2. University of Edinburgh
- 3. Beebytes Analytics CIC
- 4. INRAE Toulouse
Description
Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples collated for AmelHap using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 10 Mb. This dataset comprises the raw variant calls only for samples belonging to project accession: PRJEB16533.
Files
Files
(5.3 GB)
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md5:3dc6b8fb60014fc2a62440e8e53d8fcb
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1.3 kB | Download |
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md5:1a2bffbbe525565e2a0a6886f2bd5c85
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5.3 GB | Download |
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md5:153d329442bf70c0a77acb6f642a8f76
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189.2 kB | Download |