User: skkujin

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skkujin0
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Posts by skkujin

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Comment: C: How can I improve somatic/germline status prediction without matched normal (Pur
... Yes, right. I set "paired tumor/normal somatic counts" as raw output of Mutect without any filtering. And, I agree that filtering pair-called Mutect results by coverage, allelic fraction, supporting reads and base quality is needed like PureCN does. This filtered data should be the golden set, not ...
written 11 months ago by skkujin0
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Comment: C: How can I improve somatic/germline status prediction without matched normal (Pur
... Yes, You're right. It was outlier sample. It has extremely many SNPs compared to others. Others have 40~70 % germline likely variants. Its low prediction may be due to artifacts. I don't have any sense about artifacts now, I need to look into it. (plus I'm using Mutect 1.1.7)   In fact, I'm t ...
written 11 months ago by skkujin0
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Comment: C: How can I improve somatic/germline status prediction without matched normal (Pur
... This is one of log files. Other logs have same options. Yes, I used wgEncodeCrgMapabilityAlign100mer.bigWig and wgEncodeUwRepliSeqK562WaveSignalRep1.bigWig for making interval file like you mentioned in quick start guide. Below is cutoff I used for somatic-predicted call. ML.SOMATIC as "TRUE", FL ...
written 11 months ago by skkujin0
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How can I improve somatic/germline status prediction without matched normal (PureCN)?
... Dear Markus, Hi, I'm using PureCN for classifying somatic SNPs from germline ones without matched normal. I tested it for validation with 42 gastric cancer bam files without matched normal. They are target sequenced and its covered bed reaches 6.1Mb in all. I set muTect paired-called "SOMATIC" t ...
purecn written 11 months ago by skkujin0

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