1. Community
2. General Discussion
3. GATK Germline CNV calling

Hi Pamela Bretscher, Thank you for moving this post to the general discussion.  After running "PostprocessGermlineCNVCalls" module which is the last step of this Germline CNV caller, it generates o...

• View comment
• Krithika_Subramanian
• November 23, 2021 07:47
• 0 votes

1. Community
2. General Discussion
3. GATK Germline CNV calling

Attached screenshot  

• View comment
• Krithika_Subramanian
• November 22, 2021 12:00
• 0 votes

1. Community
2. Germline
3. GATK Variant Filtration undefined variable

Hi Pamela, Thank you for your clarification. I have given specific parameters in my command for excluding, for example, QD <2.0, SOR > 3.0, MQ < 40.0 etc.  In my input, there are variants that have...

• View comment
• Krithika_Subramanian
• October 28, 2021 04:40
• 0 votes

1. Community
2. Germline
3. GATK Variant Filtration undefined variable

Hi Pamela Bretscher, Thanks for your reply. Could you please explain me, how I can check whether VariantFiltration is applied for my data? Because there are 742,973 variants present before applying...

• View comment
• Krithika_Subramanian
• October 27, 2021 11:41
• 0 votes

1. Community
2. Germline
3. GATK Variant Filtration undefined variable

Hi Pamela Bretscher, Thanks for your reply. Here I am providing a variant line, which has the value of ReadPosRankSum or MQRankSum. Also, I am not seeing any differences after applying this filtrat...

• View comment
• Krithika_Subramanian
• October 27, 2021 05:30
• 0 votes