figshare
Browse
1/1
9 files

Mapping of ISGC SNP chip probes

Version 4 2022-01-31, 02:22
Version 3 2022-01-13, 02:11
Version 2 2019-07-02, 01:07
Version 1 2019-07-02, 01:01
dataset
posted on 2022-01-31, 02:22 authored by Rudiger BrauningRudiger Brauning
Ovine SNP chips created by the International Sheep Genomics Consortium (ISGC, https://sheephapmap.org/) were mapped onto reference genomes. Results are reported per chip and include SNP_name, chrom, pos, ref_alt, flag, rsID.

Probe sequences were taken from the Illumina manifests (ISGC_SheepLD2015_15K_20003262_A1, OvineSNP50_B, SheepHD_AgResearch_Cons_15041608_A) and mapped onto the Oarv3.1 (GCF_000298735.1) and the Rambouillet version 1 (GCF_002742125.1) and Rambouillet version 2 (GCA_016772045.1) reference genomes using bwa mem v0.7.17-r1188 with default settings. Only SNPs were mapped, indels were ignored.

For each SNP a probe pair was constructed by using AlleleA_ProbeSeq and appending either the reference or the alternative allele.
Only probe pairs where accepted that passed following filters.
-both probes have no alternative mappings
-both probes are mapped
-one probe is mapped with 0 mismatches
-both probes are not multi-mapped
-no indels were allowed
-both probes had to map in the same orientation
-both probes had to map to the same position
-mapped probes had between them exactly 1 mismatch, the SNP.

Mapped SNPs got assigned to rsIDs via their Oarv3.1 position (ftp://ftp.ensembl.org/pub/release-100/variation/vcf/ovis_aries/ovis_aries.vcf.gz).




Any data shared here is without warranty of any kind and in no event shall the authors or copyright holders be liable for any claim, damages or any liability.

History

Usage metrics

    Licence

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC