User: fongchunchan

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fongchunchan10
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fongchunchan
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Posts by fongchunchan

<prev • 13 results • page 1 of 2 • next >
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sciClone: Multiple alleles at single position
... Hi, Currently sciClone mutation input data is chr, pos, ref_reads, var_reads, vaf which assumes that we only have one a single mutated allele at a given position. Is there a way to get sciClone to work with two independent mutations at the same position? Incorporating a reference and allele colum ...
sciclone written 4 months ago by fongchunchan10 • updated 4 months ago by Chris Miller19k
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Comment: C: CNVkit: Overlapping Segments?
... Thanks. Using the `--split` option seems to have solved the overlapping intervals. ...
written 17 months ago by fongchunchan10
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Comment: C: CNVkit: Overlapping Segments?
... - 0.7.11 - Yes it's a hybrid capture and yes I used a capture targets bed file. - I am not using the --split argument - Using the default segmentation method. ...
written 18 months ago by fongchunchan10
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CNVkit: Overlapping Segments?
... After running `cnvkit.py segment`, I've noticed that some segments appear to overlap with each other. For instance, 18 18520842 60987290 BCL2 0.83552 424 131.823 18 60987231 78016748 BCL2 0.04287 175 54.1546 The end of the first segment (60,987,290) overlaps with the beginning of ...
cnvkit written 18 months ago by fongchunchan10
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CNVkit - Proper Way to Generate Accurate Sex Chromosome Predictions
... I was wondering what is the best protocol for getting accurate sex chromosomes copy number predictions? Currently I have a pool for normals of mixed gender which I am passing into the `reference` function. I don't set the `-y` option to create a male reference. There appears to be no option to actu ...
cnvkit written 18 months ago by fongchunchan10 • updated 18 months ago by Eric T.1.9k
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Comment: C: CNVkit - Format of VCF file
... Thanks for the reply. Based on the VCF header produced by the bcftools: INFO= So it would appear that the allele information is in the DP4 field and it is comma separated. This is direct output of bcftools. I'll try to use another germline mutation caller that outputs the allele data into AD. ...
written 19 months ago by fongchunchan10
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CNVkit - Format of VCF file
... I am at the step of deriving absolute integer copy number for each segment and the [documentation][1] states that one can pass in a vcf file of SNPs in the tumour samples: cnvkit.py call Sample.cns -y -v Sample.vcf -o Sample.call.cns This should extract b-allele frequencies and allow for the c ...
cnvkit written 19 months ago by fongchunchan10 • updated 19 months ago by Eric T.1.9k
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Answer: A: PyClone without copy number data
... 1) Yes there are several tools out there that can do it (e.g. TitanCNA). If possible, get parental copy number as this greatly helps PyClone. Something like TitanCNA can do this. I would look at this thread. 2) If you believe that the tumour contains little to no somatic sCNAs, then you could do th ...
written 2.0 years ago by fongchunchan10
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Somatic Mutation Calling from ddPCR
... Hi, I am working with digital droplet PCR data (http://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_6407.pdf). Essentially, the read out of such experiments are the number of "positive" and "negative" droplets for a given probe of interest. This experiment can be applied for somatic muta ...
ddpcr written 2.2 years ago by fongchunchan10
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Answer: A: Want to Skip Annotation Step (in MutSig_preprocess)
... I went with the approach of only using only the MAF file approach downloading the 4 references files and it worked for me. Have you tried that? Were you able to get it working? I am interested in trying to figure out how to build a coverage file for my dataset, but still have the pre-processing ste ...
written 2.5 years ago by fongchunchan10

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