1. Community
2. Non-Human
3. REAL Variant not called by HaplotypeCaller

Hi, I have kind of the same issue. Here is what I experienced lately and I really can't figure out a starting point. I have a sample (Sample1) that is analyzed using BWA v0.7.6a-r433 and GATK 4.1.0...

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• NawarDalila
• April 07, 2021 12:01
• 0 votes

1. Technical Documentation
2. Algorithms
3. Hard-filtering germline short variants

Chase He yes this is right.

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• NawarDalila
• March 04, 2021 09:37
• 0 votes

1. Community
2. Germline
3. How do I use MarkIlluminaAdapters properly in combination with its metrics for new adapters other than Illumina standards?

Hi Yossi Farjoun, Thanks a lot for your reply. If you take a look at the original website for the company (https://www.twistbioscience.com/resources/protocol/unique-dual-index-sequences-protocol-re...

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• NawarDalila
• October 23, 2020 08:38
• 0 votes

1. Community
2. Germline
3. How do I use MarkIlluminaAdapters properly in combination with its metrics for new adapters other than Illumina standards?

Dear Genevieve Brandt, Thanks a lot for your reply. My question was indeed about MarkIlluminaAdapters' abnormal results. Maybe I was not clear enough in that so here I try again: Are those those op...

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• NawarDalila
• October 16, 2020 05:43
• 0 votes

1. Community
2. Other
3. Fail to set up conda environment for GATK with the gatkcondaenv.yml file

Thank you very much for sharing. I will try and see what happens.

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• NawarDalila
• March 06, 2020 08:11
• 0 votes

1. Community
2. Other
3. Fail to set up conda environment for GATK with the gatkcondaenv.yml file

Hi fanwayne, Would you please share the channels that you used and how exactly you did that?  Many thanks in advance Nawar

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• NawarDalila
• March 05, 2020 13:59
• 0 votes