"NotDuplicateReadFilter" behaviour in HaplotypeCaller

Answered

Follow

sanjeevksh

• December 07, 2021 21:40

Dear Team GATK,

The description for "NotDuplicateReadFilter" read filter says it filters out reads marked as duplicate. Is it the right inference that this read filter will ONLY remove duplicate reads if these have been previously marked as 'duplicates' by some programme such as "MarkDuplicates (Picard)" OR it can automatically identify duplicate reads and remove them even if they are not marked as duplicates?

Regards,

Sanjeev

0

• 

  Genevieve Brandt (she/her)

  • December 08, 2021 18:13

  Yes, that's true. It is searching for reads marked with the 0x400 flag.

  1

  Comment actions Permalink
• 

  sanjeevksh

  • December 08, 2021 18:37

  Thanks Genevieve, that's very helpful!

  Kind regards,

  Sanjeev

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • December 08, 2021 18:44

  Good to hear!

  0

  Comment actions Permalink

Please sign in to leave a comment.