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3. Why do I see difference in ploidy in GT field within same sample after GenotypeVCFs

Hi, I actually came across this also and the study organism is diploid without any changes in ploidy expected. However, I didn't use GenomicsDBImport, just standard combinegvcfs.Do you have any ins...

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• ABours
• February 19, 2021 08:34
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3. Merge different individual VCF

Hi Linda Do, First of all, there is no CombineVariants. I think you were going for CombineGVCFs. This program is used to combine GVCFs from different samples. GATK offers two Picard tools for what ...

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• ABours
• July 07, 2020 10:16
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3. SelectVariants to get a vcf file with 1 individual from a vcf file with 3 individuals

Hi Linda Do, The only problem with your code was that you forgot to put a "-" before sn, like this "-sn". Just in case anyone else stumbles on this :) Best,

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• ABours
• July 07, 2020 10:04
• 1 vote

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3. SelectVariants v4.1.6.0 doesn't select the variants as expected

Hi Bhanu, Ok, it's nice to know that the tool does what the code says. also the confusion remains, but I can work with it. I would say I'm just questioning whether the code is logical for what one ...

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• ABours
• June 18, 2020 16:36
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3. GenotypeGvcfs has formatting issues in both v4.1.6.0 as v4.1.7.0

Hi Bhanu, Thank you for checking it, and it's good to know what's happening here. It's just striking that I didn't have this on a similar run with a different reference. Best,

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• ABours
• June 18, 2020 16:12
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3. GenotypeGvcfs has formatting issues in both v4.1.6.0 as v4.1.7.0

Hi Bhanu, I believe I shared the data (files_to_share_with_gatk_ABours.tar.gz), can you please confirm that you have? Within the snippet I ensured that the three different version of the formatting...

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• ABours
• June 10, 2020 15:19
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3. SelectVariants v4.1.6.0 doesn't select the variants as expected

Hi Bhanu, Thank you for looking into this. The command I used was (gatk4 her is v4.1.6.0): java -Xms24G -Xmx24G -jar ${gatk4} SelectVariants -R ${ref} -V final_v4.1.6.0.vcf.gz -select-type SNP -O f...

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• ABours
• June 08, 2020 07:58
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3. GenotypeGvcfs has formatting issues in both v4.1.6.0 as v4.1.7.0

Hi Bhanu, Thanks for your reply and making a ticket. But like I said, you already have a ticket for this ValidateVariants issue, to allow these lines. However, I just wanted to point out that Genot...

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• ABours
• June 02, 2020 12:13
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3. Genotyping precalled sites/variants

Hi Reto, You can actually provide a list to GenotypeGVCFs to opporate on, it's the -L function. You can specify in that list single sites. I haven't tried it, but otherwise you could take a region ...

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• ABours
• May 29, 2020 18:52
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2. Germline
3. Haplotype Caller (4.1.6.0) : java.lang.IllegalStateException: Smith-Waterman alignment failure.

Hi Bhanu, Thank you for you reply. It's a bit sad, but just to ensure I'll rerun everything in v4.1.7.0. Best,

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• ABours
• April 29, 2020 16:01
• 0 votes