Comparison of variant calling methods for whole genome sequencing data in dairy cattle

Baes, Christine F.; Dolezal, Marlies A.; Fritz-Waters, E.; Koltes, James E.; Bapst, Beat; Flury, Christine; Signer-Hasler, Heidi; Stricker, Christian; Fernando, Rohan L.; Schmitz-Hsu, Fritz; Garrick, Dorian J.; Reecy, J. M.; Gredler, Birgit (2014). Comparison of variant calling methods for whole genome sequencing data in dairy cattle In: 10th World Congress on Genetics Applied to Livestock Production. Vancouver / Canada. 17.-22.8.2014.

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Accurate identification of SNPs from next-generation sequencing data is crucial for high-quality downstream analysis. Whole genome sequence data of 65 key ancestors of genotyped Swiss dairy populations were available for investigation (24 billion reads, 96.8% mapped to UMD31, 12x coverage). Four publically available variant calling programmes were assessed and different levels of pre-calling handling for each method were tested and compared. SNP concordance was examined with Illumina’s BovineHD Genotyping BeadChip®. Depending on variant calling software used, between 16,894,054 and 22,048,382 SNP were identified (multi-sample calling). A total of 14,644,310 SNP were identified by all four variant callers (multi-sample calling). InDel counts ranged from 1,997,791 to 2,857,754; 1,708,649 InDels were identified by all four variant callers. A minimum of pre-calling data handling resulted in the highest non-reference sensitivity and the lowest non-reference discrepancy rates.

Item Type:

Conference or Workshop Item (Paper)

Division/Institute:

School of Agricultural, Forest and Food Sciences HAFL > Resource-efficient agricultural production systems

Name:

Baes, Christine F.;
Dolezal, Marlies A.;
Fritz-Waters, E.;
Koltes, James E.;
Bapst, Beat;
Flury, Christine;
Signer-Hasler, Heidi;
Stricker, Christian;
Fernando, Rohan L.;
Schmitz-Hsu, Fritz;
Garrick, Dorian J.;
Reecy, J. M. and
Gredler, Birgit

Subjects:

S Agriculture > SF Animal culture

Language:

English

Submitter:

Admin import user

Date Deposited:

10 Mar 2020 11:15

Last Modified:

10 Mar 2020 11:15

Uncontrolled Keywords:

variant calling; next generation sequencing

ARBOR DOI:

10.24451/arbor.7396

URI:

https://arbor.bfh.ch/id/eprint/7396

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