VCF file containing SNP callings for 46 Drosophila melanogaster genomes
SNPs were called using the GATK (v4.0) (McKenna et al. 2010) HaplotypeCaller best practices for variant discovery (Van der Auwera et al. 2013) over alignments generated by mapping to the iso-1 strain (Dmel_Release_6) either, the Illumina short-reads (for genomes sequenced by ONT) or Illumina-like re...
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| Tipo de recurso: | conjunto de datos |
| Fecha de publicación: | 2021 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/227749 |
| Acceso en línea: | http://hdl.handle.net/10261/227749 |
| Access Level: | acceso abierto |
| Palabra clave: | Drosophila melanogaster Variant calling SNPs Genomics Transposable Elements Drosophila Melanogaster Rech 2021 |
| Sumario: | SNPs were called using the GATK (v4.0) (McKenna et al. 2010) HaplotypeCaller best practices for variant discovery (Van der Auwera et al. 2013) over alignments generated by mapping to the iso-1 strain (Dmel_Release_6) either, the Illumina short-reads (for genomes sequenced by ONT) or Illumina-like reads generated using randomreads.sh from BBTools (Bushnell) from the corrected PacBio reads. After running the GATK HaplotypeCaller for each genome, we merged them using the CombineGVCFs command and we performed the joint genotyping using GenotypeGVCFs. We kept only biallelic SNPs using the GATK command SelectVariants (parameters -select-type SNP --restrict-alleles-to BIALLELIC). Finally, we removed SNPs with missing data in at least one genome, resulting in a total of 2,797,589 SNPs. Since selscan methods assume phased haplotypes, we used SHAPEIT4 (Delaneau et al. 2019) for determining haplotypes in the SNP data. We adapted the vcf format to the expected by SHAPEIT4 (Delaneau et al. 2019) and we created a genetic map file based on the recombination rates calculated by (Comeron et al. 2012) and the genetic positions available in FlyBase (https://wiki.flybase.org/wiki/FlyBase:Maps, last updated June 15, 2016). We then indexed vcf files using bcftools index (v1.9) (Li 2011) and run SHAPEIT4 for each chromosomal arm separately. Raw data (long and short read sequencing) have been deposited in NCBI under the BioProject accession PRJNA559813. |
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