User: ernfrid

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ernfrid380
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Saint Louis
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2 years, 11 months ago
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5 years, 6 months ago
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Posts by ernfrid

<prev • 64 results • page 1 of 7 • next >
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Answer: A: BreakDancer is giving blank output!
... As far as I know the original BreakDancer perl script is unmaintained at this point. You may want to try using the latest version: https://github.com/genome/breakdancer/tree/v1.4.5 ...
written 2.9 years ago by ernfrid380
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Comment: C: Expect Library - Bam-Readcount
... Only in the file of positions should there be no header. You definitely want to keep the header of your BAM file. ...
written 3.0 years ago by ernfrid380
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Comment: C: Need help understanding read depth for somaticsniper vcf's
... BCOUNT for your example is (0,5,9,0). There are two bugs going on here. BCOUNT is being limited to only bases seen in called tumor and normal genotypes. The limitation in 1 is only being applied in a way that non-ACTG bases can count in multiple categories. Thus, your T isn't being cou ...
written 3.4 years ago by ernfrid380
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Comment: C: Need help understanding read depth for somaticsniper vcf's
... My guess would be 3 reads with Ns for 871092? Is that right? One reason the BCOUNT seems to make no sense is that you're actually looking at the DP4 counts. It still won't make sense because there are bugs relating to how the counts are generated. Ns are being double counted in all categories and a ...
written 3.4 years ago by ernfrid380
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Comment: C: Need help understanding read depth for somaticsniper vcf's
... I'm a bit baffled why this might be happening. I do think it likely this is a bug. The tumor depth should match the DP4 counts. I do see what I think is a bug in how the BCOUNT is calculated. My best guess for DP4 is that there might be some Ns in your reads? Would it be possible to see samtools mpi ...
written 3.4 years ago by ernfrid380
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Comment: C: Breakdancer inaccurate output.
... Thanks Fernando. I suspect that this is an issue with BWA mem chimeric alignments. Can you post how you ran BWA mem (what command line arguments)? ...
written 3.4 years ago by ernfrid380
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Answer: A: Breakdancer inaccurate output.
... My best guess is that this is a bug. There are much, much newer versions of breakdancer available at this point. I would suggest trying the latest available via github (see: https://github.com/genome/breakdancer/releases). ...
written 3.4 years ago by ernfrid380
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Answer: A: what is the ”indel pileup file“ needed for somaticsniper fpfilter
... You should use the tumor BAM and run samtools pileup as so: samtools pileup -cvi -f $reference $tumor_bam > $indel_pileup_file ...
written 3.4 years ago by ernfrid380
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Answer: A: Breakdancer Max Kahan Error:0
... That is a status message. It is shown every time that BreakDancer runs and does not indicate that BreakDancer had a problem while it was running. Your results are valid. We will consider changing the wording of that message or removing it all together. ...
written 3.6 years ago by ernfrid380
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Comment: C: Somaticsniper Hangs Up
... I'm interested in learning more about the bug here, but I don't think transferring the whole BAM is feasible. 40Gb is quite sizable for troubleshooting. In addition, I'm concerned about transferring human sequencing data around with regards to data protection and access permissions. In the past, we ...
written 3.7 years ago by ernfrid380

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Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Breakdancer Max Kahan Error:0

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