User: Zoey Zou

gravatar for Zoey Zou
Zoey Zou40
Reputation:
40
Status:
New User
Location:
Australia
Last seen:
1 year, 2 months ago
Joined:
1 year, 5 months ago
Email:
z********@gmail.com

A beginner in tumor phylogenetics

Posts by Zoey Zou

<prev • 7 results • page 1 of 1 • next >
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Comment: C: the difference between the positions called by somatic caller (MuTect2) and the
... Hi, Thanks for your reply ( Sorry for my mistake, I have corrected it). Do you mean that the joint calling are more likely to remove those low frequency variants when comparing to the somatic calling? ...
written 17 months ago by Zoey Zou40
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Comment: C: vcftools Warning: Expected at least 2 parts in FORMAT entry
... Hi, I just got the reply about this question from the github (https://github.com/vcftools/vcftools/issues/134). If you are still having that problem you can have a look. ...
written 17 months ago by Zoey Zou40
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the difference between the positions called by somatic caller (MuTect2) and the position called by germline caller (UnifiedGenotyper)?
... Hi, I am new to tumor phylogenetics. I want to call snvs from the tumor cells and using the snvs to build the phylogenetic trees. I found that currently there are two ways to call somatic mutations from tumor samples. One is doing the somatic calling using somatic caller (MuTect2, Varscan ..). ...
somatic calling snv germline calling written 17 months ago by Zoey Zou40
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Comment: C: vcftools Warning: Expected at least 2 parts in FORMAT entry
... Parameters as interpreted: (just use the simplest parameter for testing) --gzvcf 16011.vcf.gz --recode --remove-filtered-all --stdout ...
written 17 months ago by Zoey Zou40
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vcftools Warning: Expected at least 2 parts in FORMAT entry
... Hi all, I have used the vcftools to filter my data some weeks ago, and it went smoothly. However, I run the vcftools with the same vcf file again recently, it gets the following warnings: Using zlib version: 1.2.8 Warning: Expected at least 2 parts in FORMAT entry: ID=PGT,Number=1,Type=Str ...
vcftools written 17 months ago by Zoey Zou40
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Comment: C: can VarScan2 do joint somatic calling?
... Hi, Appreciate for your help. I just realized that I did not have a good understanding of somatic calling. And I found that in the GATK website it explained that "there is currently no way to perform joint calling for somatic variant discovery". Maybe I can find another method to put the snvs togeth ...
written 18 months ago by Zoey Zou40
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can VarScan2 do joint somatic calling?
... Hi, In my project, I am going to use the SNVs of different tumor regions to build the phylogenetic tree for that tumor. I am doing joint calling in different software separately. Now, I want to try VarScan2. I have one normal bam file and 10 tumor bam files from that patient. But I find that the im ...
varscan somatic calling snp written 18 months ago by Zoey Zou40

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Supporter 17 months ago, voted at least 25 times.

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