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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comparison-variant-calling-methods-whole-genome-sequencing-data-dairy-cattle.pdf - Published Version Available under License Creative Commons: Attribution-Noncommercial-No Derivative Works (CC-BY-NC-ND). Download (233kB) | Preview |
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) |
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Division/Institute: |
School of Agricultural, Forest and Food Sciences HAFL > Resource-efficient agricultural production systems School of Agricultural, Forest and Food Sciences HAFL > Agriculture |
Name: |
Baes, Christine F.; Dolezal, Marlies A.; Fritz-Waters, E.; Koltes, James E.; Bapst, Beat; Flury, Christine; Signer-Hasler, Heidi  0000-0001-5193-5306; 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: |
Service Account |
Date Deposited: |
10 Mar 2020 11:15 |
Last Modified: |
18 Dec 2020 13:28 |
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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