User: geneart$$

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geneart$$40
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Posts by geneart$$

<prev • 55 results • page 2 of 6 • next >
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Comment: A: VQSR no r file being created
... Thankyou Jeremy and rbagnall for your replies ! Yes the VQSR actually ran for a bit but gave me a truncated file so the end of the file actually had not shown the memory used although it did say : Tool returned: true" It was indeed the backslash that I had missed !! Small annoying things...but than ...
written 6 weeks ago by geneart$$40
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Comment: C: VQSR no r file being created
... Thankyou for the reply Jeremy, but thats not it. I tried with the -- and yet no rscript file is generated ! ...
written 7 weeks ago by geneart$$40
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VQSR no r file being created
... Hi , I have r module loaded in the path I am running my scripts , yet the `--rscript all_jointcalls.AS.plots.R` is not even created ! Is there something I am missing? Here is my command and I am running GATK/4.1.8.0 gatk VariantRecalibrator \ -V ../all_jointcalls_sorted.vcf \ -A ...
gatk vqsr written 7 weeks ago by geneart$$40
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Understanding GATK evaluation metrics
... Hi all, I recently implemented GATK pipeline on a small set of samples (WES) and did hard filtering as I had only 10 samples and got the GATK to spit out the metrics file. I used the default filtering parameters for the first pass and this is the command: gatk VariantFiltration \ -V myfa ...
gatk next-gen metrics snp written 9 weeks ago by geneart$$40
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Answer: A: VariantEval GATK error
... Ok folks, So variant evaluation worked ! It was my dbsnp vcf I was using, for -D option. I should have extracted the subset chromosomes of interest, from the dbsnp GATK resource bundle original vcf file and used that as a -D option. Instead, I was using the entire original dbsnp.vcf with all th ...
written 10 weeks ago by geneart$$40
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Comment: C: VariantEval GATK error
... Update on my posted issue: I don’t still quite understand why I am getting eval error at chrX. so I went through my input again. 1. I had specifically extracted few chromosomes only and made my genomicsDB and called joint genotype and then sorted that file and pushed through eval.  2. However the ...
written 10 weeks ago by geneart$$40
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VariantEval GATK error
... Hi  First of, pardon my dual post of the same on GATK and here. I understand that GATK guys may not answer this in time also provided this is on a sat night and I am in super time crunch to get some evaluation metrics by monday and hence in a desperation I am seeking help here as well. So my apol ...
variant calling gatk error germline written 10 weeks ago by geneart$$40
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Comment: C: GATK GenomicsDBImport - use list as input
... oops ! placed this in the wrong place. should be after Bari.ballew's comment ! my bad! but you get it .... :) ...
written 11 weeks ago by geneart$$40
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Comment: A: GATK GenomicsDBImport - use list as input
... Hi Bari.ballew, We could also do this as: for i in *.vcf.gz; do echo `bcftools query -l $i`;echo $i;done | paste - - Either of the scripts gives me output as below: sample_11 sample_11_HCcalls.g.vcf.gz sample_23 sample_23_HCcalls.g.vcf.gz sample_9 sample_9_HCcalls.g.vc ...
written 11 weeks ago by geneart$$40
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Comment: C: GATK variant calling
... @brunobsouzaa, thankyou for your reply . Yes I have a bed file. So I dont have to do jointcalls from GATK then, is what you are suggesting? ...
written 11 weeks ago by geneart$$40

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