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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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GoodCigarReadFilter Follow

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GATK Team
  • Updated

Keep only reads containing good CIGAR string

Category Read Filters

Overview

Keep only reads containing good CIGAR strings.

Good CIGAR strings have the following properties:

  • Valid according to the SAM specifications.
  • Does not start or end with deletions (with or without preceding clips).
  • Does not have consecutive deletion/insertion operators.

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GATK version 4.2.0.0-SNAPSHOT built at Mon, 22 Feb 2021 13:44:49 -0800.

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    chenglei

    Can you 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

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