User: tjbencomo

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tjbencomo10
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Posts by tjbencomo

<prev • 5 results • page 1 of 1 • next >
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Interpretting cnvkit p-value results
... I'm using `cnvkit` to analyze several tumors sequenced via WGS without any normal controls. I've analyzed the samples with the following command cnvkit.py batch RWRB*.tumor.bam \ -n -p $NCORES \ -f $PI_HOME/refs/hg38/Homo_sapiens_assembly38.fasta \ --annotate refFlat.txt \ --dro ...
cnvkit cnv written 3 months ago by tjbencomo10 • updated 4 weeks ago by Biostar ♦♦ 20
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Answer: A: Publicly Available WGS Samples for Panel of Normals?
... I ended up using the hg38 1000 Genomes PON from the Broad linked to by @RamRS. Although the PON was most likely generated from samples sequenced using different prep protocols, one of the GATK developers says on the [GATK forum](https://gatk.broadinstitute.org/hc/en-us/community/posts/360061543792-P ...
written 5 months ago by tjbencomo10
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Comment: C: Publicly Available WGS Samples for Panel of Normals?
... I forget to mention I plan to run Mutect2 with a PoN and gnomAD to filter for germline variants. Would it be correct to say VarScan2 does the same thing as Mutect2 with the gnomAD VCF - filter germline variants using gnomAD? ...
written 5 months ago by tjbencomo10
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Comment: C: Publicly Available WGS Samples for Panel of Normals?
... It was my understanding that the PoN should consist of samples that were sequenced in a similar way to my own samples. I guess using the 1000g PoN could seem reasonable (although the assumption there is that their prep kit/sequencer is similar to mine - probably not a bad although not optimal assump ...
written 5 months ago by tjbencomo10
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Publicly Available WGS Samples for Panel of Normals?
... I have 15 tumors that were sequenced using whole genome sequencing at 30x depth. I would like to identify somatic variants using Mutect2. Unfortunately we don't have any normal samples, so I would like to build a Panel of Normals to use with Mutect2 in tumor-only to identify somatic variants. I also ...
wgs snp sequencing written 5 months ago by tjbencomo10

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