User: clfougner

gravatar for clfougner
clfougner60
Reputation:
60
Status:
New User
Location:
Institute for Cancer Research, Oslo University Hospital, Norway
Website:
https://github.com/clf...
Last seen:
1 month, 2 weeks ago
Joined:
1 year, 8 months ago
Email:
c********@gmail.com

Posts by clfougner

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Very few somatic mutations/variants using GATK's best practices (mouse exome seq
... Quick update: I've figured out the (now somewhat embarrassing) issue! I'd been using a placeholder for the read group names (which I figured was inconsequential because it's "just" a name), which was the same for tumor and and normal samples. Once I started using the proper read group names, I've st ...
written 17 months ago by clfougner60
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Comment: C: Very few somatic mutations/variants using GATK's best practices (mouse exome seq
... Thanks for the quick response! My data has a 100x coverage. As with any tumor I'm sure there's some normal cell contamination, but the tumors were harvested from mice and the contamination should be low. 1) I ran VarScan overnight, and I got a list of over 4000 variants. Definitely seems more odd ...
written 17 months ago by clfougner60
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Very few somatic mutations/variants using GATK's best practices (mouse exome sequencing)
... I'm working on somatic variant calling from mouse exome sequencing data, and my pipeline is based off of GATK's best practices. I have the entire pipeline set up, from FASTQ files to VCF files, including all preprocessing. However, when I run it, only 1-3 variants come out that pass MuTect's filters ...
exome gatk mouse mutect sequencing written 17 months ago by clfougner60
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Comment: C: mm10 SNP/Indel database for realignment around indels
... Success! Don't know what the issue was, but I ran the code from paste.ofcode on my lab's server (instead of my own computer) and it worked, so it must have been something with my runtime environment. Trying the RealignerTargetCreator now and it seems to be working. Thanks a lot! ...
written 20 months ago by clfougner60
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Comment: C: mm10 SNP/Indel database for realignment around indels
... Hmm, I'm still getting an error when I try running it: awk: syntax error at source line 1 context is { if($0 !~ /^#/) print "chr"$0; else >>> if(match($0,/(##contig= ...
written 20 months ago by clfougner60
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Comment: C: mm10 SNP/Indel database for realignment around indels
... Thanks so much for the answer! Unfortunately, when I run this code: awk '{ if($0 !~ /^#/) print "chr"$0; else if(match($0,/(##contig= mm10.INDELS.vcf I get the following error: awk: non-terminated regular expression (##contig=... at source line 1 context is >>> < ...
written 20 months ago by clfougner60
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mm10 SNP/Indel database for realignment around indels
... Hi, I'm following the Broad Institute's best practices for variant calling using the Genome Analysis Toolkit, and am having issues with the realignment around indels. Specifically, my issue pertains to the use of the RealignerTargetCreator. Briefly, my preprocessing so far consists of mapping the ...
exome mouse sequencing dbsnp gatk written 20 months ago by clfougner60 • updated 20 months ago by John12k

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Popular Question 15 months ago, created a question with more than 1,000 views. For mm10 SNP/Indel database for realignment around indels

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