Do BAM file must have marked duplicates for germline CNV analysis?

Answered

Follow

Ju Jose

• April 05, 2022 16:52

Hello all,

I am using GATK 4.2.5.0 for gCNV analysis of hundreds of exomes, and I can´t figure out if BAM input files must have the read duplicates marked or not for the default germline CNV analysis.

0

• 

  Genevieve Brandt (she/her)

  • April 06, 2022 01:36

  Hi Ju Jose,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Genevieve

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • April 12, 2022 19:47

  Hi Ju Jose,

  Thank you for your question. MarkDuplicates is recommended in data pre-processing for all types of variant calling.

  You can read more about it here: Data pre-processing for variant discovery.

  Let me know if you have any further questions.

  Best,

  Genevieve

  0

  Comment actions Permalink

Please sign in to leave a comment.