ABours
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Activity overview
Latest activity by ABours-
ABours commented,
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 commented,
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 commented,
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 commented,
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 commented,
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 commented,
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 commented,
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 created a post,
SelectVariants v4.1.6.0 doesn't select the variants as expected
AnsweredHi, I'm subsetting the vcf that I got from GenotypeGVCFs into separate SNP and INDEL vcfs (to hard-filter), with SelectVariants from GATK version 4.1.6.0. However, the program doesn't behave how I ...
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ABours commented,
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 commented,
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 ...