what is a Good Cigar?

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chenglei

• July 02, 2022 06:25

gatk BaseRecalibrator module has a  parameter named "GoodCigarReadFilter", Can anyone explain what is a good cigar string more specifically？ 150M is a good cigar, then what about 10S100M40H? I did not find a good explaination in SAM specifications. Hope your response! Appreciate!

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  Anthony Dias-Ciarla

  • July 05, 2022 14:10

  Thank you for your post, chenglei ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

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  Anthony Dias-Ciarla

  • July 05, 2022 14:25

  Hi Chenglei,

  Thank you again for writing to the GATK forum. We hope to be able to clarify your question.

  Please find some useful links below.

  1. Properties of good CIGAR strings
  2. BaseRecalibrator tool index

  I hope these resources help. Please let us know if you have any further questions.

  Best,

  Anthony

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