Published June 20, 2022
| Version 1.1.0
Dataset
Open
PRJEB39369 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: PRJEB39369.
Files
Files
(2.4 GB)
| Name | Size | Download all |
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md5:e97f32c694798277a67cb9972d21ac07
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495 Bytes | Download |
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md5:5b40a6e596c30561606f5ac46eb67e06
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2.4 GB | Download |
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md5:a97925f0d4c057696b6ee6222241bdf0
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183.8 kB | Download |