User: geneart$$

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geneart$$20
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Posts by geneart$$

<prev • 51 results • page 1 of 6 • next >
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Answer: A: Variant filtration on lowGQ values
... Update on my issue above: The file I made by grep that has such low number of variants is because , for some bizzarre reason it is also removing GQ that are >20 randomly ! I cant figure out why! Not sure what is going on ! So I went ahead with vcf tools but I still see the rows with "Filter_GQ- ...
written 4 days ago by geneart$$20
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Comment: C: Variant filtration on lowGQ values
... Hi Pierre, THankyou for taking time to reply! I did take a look at the file before filtering and after filtering. Yes I had counted without the header. The reason you are seeing the oneliner in my earlier post without a grep -v "##" is cos when we use grep to filter out vcf files the header follo ...
written 4 days ago by geneart$$20
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Variant filtration on lowGQ values
... Hi all, I have a vcf that I made by followign GATK best practices workflow and I filtered genotypes with low GQ < 20. However I understand that they are not removed instead they are tagged as "FILTER_GQ_20" in my vcf. gatk VariantFiltration \ -V all_jointcalls_sRecal_allPASS_PP.vcf ...
gatk genotype filtering written 4 days ago by geneart$$20
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GATK VQSR output
... Hi, I performed VQSR on SNPS and then used that file to do VQSR on Indels. The tranches file ouput looks like this: targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,model,accessibleTruthSites,callsAtTruthSites,truthSensitivity 99.95,316,219,0.0000,0.0000,2.1 ...
gatk applyvqsr written 9 days ago by geneart$$20
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Answer: A: Is it possible to use VariantRecalibrator with only one sample? (90,000 MuTect2
... Hi wiki, VQSR is not recommended to be used when you have less number of samples and definitely not when you have 1 sample. Please see :https://gatk.broadinstitute.org/hc/en-us/articles/360037594511 However , you can pad the samples using samples from good database source like 1000G. GATK explains h ...
written 9 days ago by geneart$$20
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Answer: A: How Do I Use Variantfiltration To Filter By Vqslod And/Or The Tranches?
... I understand it has been a long time since this discussion here, but this has raised a similar question in me. I have the tranches file generated from VQSR, however based on the tranch plot itself, I would pick 99.9 tranch to go to applyVQSR, as the TP is better in the 99.9 tranch based on the p ...
written 11 days ago by geneart$$20
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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 11 days ago by geneart$$20
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Comment: C: VQSR no r file being created
... Thankyou for the reply Jeremy, but thats not it. I tried with the -- and yet no rscript file is generated ! ...
written 12 days ago by geneart$$20
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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 12 days ago by geneart$$20
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Understanding GATK evaluation metrics
... Hi all, I recently implemented GATK pipeline on a small set of samples (WES) and did hard filtering as I had only 10 samples and got the GATK to spit out the metrics file. I used the default filtering parameters for the first pass and this is the command: gatk VariantFiltration \ -V myfa ...
gatk next-gen metrics snp written 27 days ago by geneart$$20

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