User: newDNASeqer

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newDNASeqer630
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Posts by newDNASeqer

<prev • 68 results • page 1 of 7 • next >
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Comment: C: Dissecting number of forward/reverse reads from GATK output
... when I try to use VariantAnnotator, I got the following error. I guess it no longer works with SB annotation. Looks like I'll have to re-run the HaplotypeCaller. I am using GATK 3.2   StrandBiasBySample can only be used with likelihood based annotations in the HaplotypeCaller ...
written 4.9 years ago by newDNASeqer630
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Dissecting number of forward/reverse reads from GATK output
... We use GATK to make variant callings on exome-seq dataset, and recently we need to know the number of forward and reverse reads that cover the mutations identified by GATK. However, GATK's output (vcf) does not contain such information.  I am thinking about using the mutation position as reported i ...
reads gatk written 4.9 years ago by newDNASeqer630 • updated 4.9 years ago by Raony Guimarães990
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Inferring zygosity information from MAF
... I've heard that we can't infer heterozygosity or homozygosity for the mutations identified in MAF files, but I noticed that the MAF file's columns 11-13 may have information for inferring this info. For example Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 G G C ...
maf written 5.0 years ago by newDNASeqer630 • updated 4.9 years ago by Cyriac Kandoth5.3k
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annotating MAF files
... I've read quite a few posts on this forum on MAF files: https://www.biostars.org/p/69222/ and https://www.biostars.org/p/74822/ But one thing I do not understand is why people would want to convert VCF to MAF format. My understanding on VCF files is that they can be annotated by tools such as Anno ...
maf annotation written 5.0 years ago by newDNASeqer630 • updated 4.9 years ago by Cyriac Kandoth5.3k
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Downloadable database for human pathways and the associated genes
... I've been looking to download human signaling pathways & gene set database. I see that pantherdb.org offers such dataset for download, and I am able to extract signaling pathways and their associated genes, and save them in my local database. However, I noticed that the gene symbols may not the ...
pathway database written 5.1 years ago by newDNASeqer630 • updated 5.1 years ago by Christian2.8k
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What is ref sequence name in BAM file header ?
... I am trying to use cn.mops to make CNV calls on my BWA-aligned BAM files, the getReadCountsFromBAM() function has an option for "seqRefName", and the explanation for this field is:   Name of the reference sequence that should be analyzed. The name must appear in the header of the BAM file. If it i ...
cn.mops cnv written 5.1 years ago by newDNASeqer630 • updated 5.1 years ago by Devon Ryan90k
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Comment: C: How to make this kind of 3-D plotting for cancer subclones ? (picture attached)
... Thanks Chris for the reply. I had fractional VAFs (between 0 and 1) in my files for the sciClone plotting posted above this, however, after I converted them to percentage, I think I got better looking plots. I have uploaded two captured plots for you to see, however, I still need your help with int ...
written 5.1 years ago by newDNASeqer630
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Comment: C: How to make this kind of 3-D plotting for cancer subclones ? (picture attached)
... @Chris Miller, thanks for your reply.  Yes, I've tried to use your sciClone software, and below is what I got from my preliminary attempts using two of my samples. As you see, the clusters are too close, I was wondering if there's any way to change the scale of the X-axis so that I can make the clu ...
written 5.1 years ago by newDNASeqer630
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Comment: C: How to make this kind of 3-D plotting for cancer subclones ? (picture attached)
... thanks Noushin, but that last sentence is too terse for me to repeat how they did it :( ...
written 5.1 years ago by newDNASeqer630
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How to make this kind of 3-D plotting for cancer subclones ? (picture attached)
... I am interested in making 3-D plotting like this below picture for illustrating the subclones/clustered mutations of cancer cells. I have exome-seq data and have calculated the VAFs (Variant Allele Frequency), but I have no idea how to do the plotting. Does anyone know what software of package can d ...
heterogeneity subclone cancer written 5.1 years ago by newDNASeqer630 • updated 2.6 years ago by Biostar ♦♦ 20

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