hi, everyone, i always have a question about the detailed algorithms used in gatk re-alignment step. i looked through the GATK documents but did not find useful information. the only thing useful i found is in the GATK wrokshop, https://drive.google.com/drive/folders/0BwTg3aXzGxEDN0pTMzV2aGFlQ2M, Realignment around indels in 8th ppt：1）Finds minimum alternate consensus sequence(s) that best fits reads；2）score for alternate consensus uses sum of quality scores of mismatching bases; 3)If best alternate consensus is sufficiently beher than the original alignments -> accept proposed realignment。can someone provide more detailed info about re-align in GATK. thanks a lot.
Question: algorithm of gatk re-alignment
13 days ago by
lffu_0032 • 30
lffu_0032 • 30 wrote:
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