User: geneart$$

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geneart$$40
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Posts by geneart$$

<prev • 55 results • page 1 of 6 • next >
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Comment: C: VariantToTable not calling HET HOM etc
... Kevin, my apologies. Your code works fine. Too many things happening simultaneously for me ! going crazy ! The output I was mentioning was from using bcftools stats and that is where I am getting variations. I cant understand why bcftools would miss a couple counts. I dont have much experience w ...
written 8 weeks ago by geneart$$40
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Comment: C: VariantToTable not calling HET HOM etc
... Hi Kevin, I tried your code from the link above A: How to get sample names and genotype for SNP in multi-sample VCF file and it works well and does what I need. However I noticed a small discrepancy. I have total of 2931 variants across all my samples in my cohort across 8 genes I am interested in. ...
written 8 weeks ago by geneart$$40 • updated 8 weeks ago by Kevin Blighe67k
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Comment: C: VariantToTable not calling HET HOM etc
... Thankyou Kevin. Maybe GATK variantsToTable works well with single sample vcf rather than multi sample vcf. I did go through your code from the links posted and that was great ! Thankyou so much! ...
written 8 weeks ago by geneart$$40
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VariantToTable not calling HET HOM etc
... Hi all, I was trying to get stats on # HOM VAR #HET etc from my vcf file using `VariantsToTable`. As below: gatk VariantsToTable -R /hg38/Homo_sapiens_assembly38.fasta \ -V all_jointcalls_annRegion.vcf \ -F CHROM -F ID -F POS -F REF -F ALT -F QUAL -F DP \ -GF GT -GF GQ -GF HE ...
gatk variantstotable written 9 weeks ago by geneart$$40 • updated 9 weeks ago by _r_am30k
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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 10 weeks ago by geneart$$40
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Comment: C: Variant filtration on lowGQ values
... Hi Pierre, THankyou for taking time to reply! I did take a look at the file before filtering and after filtering. Yes I had counted without the header. The reason you are seeing the oneliner in my earlier post without a grep -v "##" is cos when we use grep to filter out vcf files the header follo ...
written 10 weeks ago by geneart$$40
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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 10 weeks ago by geneart$$40
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GATK VQSR output
... Hi, I performed VQSR on SNPS and then used that file to do VQSR on Indels. The tranches file ouput looks like this: targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,model,accessibleTruthSites,callsAtTruthSites,truthSensitivity 99.95,316,219,0.0000,0.0000,2.1 ...
gatk applyvqsr written 11 weeks ago by geneart$$40
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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 11 weeks ago by geneart$$40
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Answer: A: How Do I Use Variantfiltration To Filter By Vqslod And/Or The Tranches?
... I understand it has been a long time since this discussion here, but this has raised a similar question in me. I have the tranches file generated from VQSR, however based on the tranch plot itself, I would pick 99.9 tranch to go to applyVQSR, as the TP is better in the 99.9 tranch based on the p ...
written 11 weeks ago by geneart$$40

Latest awards to geneart$$

Great Question 7 weeks ago, created a question with more than 5,000 views. For EdgeR toptags question
Great Question 3.1 years ago, created a question with more than 5,000 views. For EdgeR toptags question
Popular Question 3.1 years ago, created a question with more than 1,000 views. For SAM File target extraction
Popular Question 5.7 years ago, created a question with more than 1,000 views. For SAM File target extraction
Popular Question 5.7 years ago, created a question with more than 1,000 views. For EdgeR toptags question
Popular Question 5.7 years ago, created a question with more than 1,000 views. For miRNA names from ensemble IDs

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