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Small variant detection

JL Jeong Hoon Lee
SK Solbi Kweon
YP Yu Rang Park
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After preprocessing the DNA sequencing data, we detected single nucleotide variants (SNVs) using three algorithms. VarScan and GATK HaplotypeCaller (HC) were used to find genetic variants between the sample DNA sequence compared with the reference sequence35. Somatic variants were called using GATK MuTect236. Variants called by a mixture of germline and somatic variant calling tools were compared based on the assumption that NGS pipeline information was not properly shared during the communication process for the genetic variant of the patient. Reference genome databases, dbSNP build 138, and COSMIC, a source of commonly mutated genes, were used for the variant-calling argument.

Copyright and License information: The Author(s) ©2021
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