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alexdobin / STAR

RNA-seq aligner
MIT License
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STAR and GATK #1816

Open DaliBAmor opened 1 year ago

DaliBAmor commented 1 year ago

Hello Alex, I want to detect germline variant using GATK as it's described in this pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- ) Could we use STAR instead of BWA to map the genome and then apply GATK or only bwa could be used for germline mutations ?

thank you

alexdobin commented 1 year ago

Hi @DaliBAmor

it's possible, in principle. However, STAR main application is mapping RNA (spliced) reads, and it will not be as accurate as BWA for mapping DNA reads.