1. Announcements
2. Blog
3. DRAGEN-GATK Update: Let's get more specific

Hi Niko Balanis   Very glad and excited to hear that you are already getting started with this! Here is the script that was used to filter the GATK variants: https://github.com/broadinstitute/gatk/...

• View comment
• Bhanu Gandham
• August 05, 2020 16:16
• 0 votes

1. Community
2. Other
3. MarkDuplicatesSparks not removing some duplicates?

Hi Tom Morrison My sincere apologies for the delay in getting back to you. This question fell off my radar. I will however prioritize it now.   I took a look at the data you shared with us. I am lo...

• View comment
• Bhanu Gandham
• August 03, 2020 04:42
• 0 votes

1. Community
2. Germline
3. DP/AD in SNP greater than coverage in bamout?

Hi mk   We are looking into this and will get back to you shortly.

• View comment
• Bhanu Gandham
• July 21, 2020 17:25
• 0 votes

1. Community
2. Non-Human
3. Why does --sample-ploidy/-ploidy option not work in HaplotypeCaller or GenotypeGVCFs?

HI Mark Farman   I checked with our dev team and this is what they said: HaplotypeCaller is expecting messy reads that may not always align correctly. In that situation, even in a haploid organism,...

• View comment
• Bhanu Gandham
• July 14, 2020 19:49
• 0 votes

1. Community
2. Non-Human
3. Why does --sample-ploidy/-ploidy option not work in HaplotypeCaller or GenotypeGVCFs?

Hi Mark Farman   Sorry for the delay. We are looking into this and will get back to you shortly.

• View comment
• Bhanu Gandham
• July 14, 2020 14:26
• 0 votes

1. Community
2. Other
3. MarkDuplicatesSparks not removing some duplicates?

Hi Tom Morrison   We reproduce results on our end once we have exhausted all other options. Can you please provide the mate pairs alignments of the reads you think should be filtered out? As mentio...

• View comment
• Bhanu Gandham
• July 13, 2020 03:37
• 0 votes

1. Community
2. Somatic
3. Mutect2 doesn't produce stats file

Serena Ferraresso   This is weird. This issue is almost always resolved by recreating the fasta file. As mentioned by you earlier, maybe this issue is because of the old version of samtools you are...

• View comment
• Bhanu Gandham
• July 11, 2020 16:39
• 0 votes

1. Community
2. Other
3. MarkDuplicatesSparks not removing some duplicates?

Hi Tom Morrison I have a couple of suggestions for you to try,  Can you please try to run it with MarkDuplicates instead of MarkDuplicatesSpark and see if that makes any difference? Try to run the...

• View comment
• Bhanu Gandham
• July 11, 2020 16:03
• 0 votes

1. Community
2. Other
3. Merge different individual VCF

HI ABours   Thank you so much for your input!

• View comment
• Bhanu Gandham
• July 07, 2020 17:53
• 0 votes