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 9 weeks 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 9 weeks 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 9 weeks 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 9 weeks ago by skkujin0

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