User: BAGeno

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BAGeno140
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Posts by BAGeno

<prev • 83 results • page 1 of 9 • next >
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Contra control file
... Hi, I am want to find copy number variations in my exome sequencing data. For this purpose i would like to use `contra`. I do not have control bam so can I use bam file of 1000 genome as my control? ...
contra cnv written 18 days ago by BAGeno140 • updated 17 days ago by kanika.15180
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Comment: C: Tranche Plot after VSQR
... @Nicolas Is ![this ][1] OK? Should I make `--truth-sensitivity-filter-level` 99.9 in `ApplyVQSR`. [1]: https://drive.google.com/file/d/1z18aycmkL3PE3yM3Pe_sFeDC6t3nTTR_/view?usp=sharing ...
written 5 weeks ago by BAGeno140
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Comment: C: Tranche Plot after VSQR
... @Nicolas I have made GVCF with interval file having size of about 400MB. Previously their size of 3 GB. Is this right or I am making mistake somewhere? ...
written 6 weeks ago by BAGeno140
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Comment: C: Tranche Plot after VSQR
... Is it necessary to include 1000 genomes bam? As I have machine of low RAM ...
written 7 weeks ago by BAGeno140
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Comment: C: Tranche Plot after VSQR
... I have used GATK 4.0.8. I run `HaplotypeCaller`, `CombineGVCFs`, and `GenotypeGVCFs`. I did not use interval file. So what should I do for this? ...
written 7 weeks ago by BAGeno140
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Tranche Plot after VSQR
... Hi I am doing exome sequencing of 15 patients. After variant calling I run `VariantRecalibrator` using this command gatk VariantRecalibrator -R new_hg38.fa \ -V allsample.vcf \ --resource hapmap,known=false,training=true,truth=true,prior=15.0:hapmap_3.3.hg38.vcf.gz \ --resourc ...
gatk4 variantreclibration written 7 weeks ago by BAGeno140 • updated 7 weeks ago by Nicolas Rosewick8.3k
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Comment: C: Vcf produced after ApplyVSQR step
... This data is of exome sequencing ...
written 7 weeks ago by BAGeno140
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Comment: C: Vcf produced after ApplyVSQR step
... [This is my tranches pdf file.][1] Can you please tell me if its fine? [1]: https://drive.google.com/open?id=1No-XbyODuyrdQF2UtLeT6RLr4dI3sN2t ...
written 9 weeks ago by BAGeno140
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Comment: C: Vcf produced after ApplyVSQR step
... Could you please tell me how should I plot graphs? I have R script made by `VariantRecalibrator` and also downloaded `ggplot2` in R. ...
written 9 weeks ago by BAGeno140
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Comment: C: Vcf produced after ApplyVSQR step
... So should I filter any sites which are not in my defined range of tranches? ...
written 9 weeks ago by BAGeno140

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Supporter 7 weeks ago, voted at least 25 times.
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