User: ryan.hartmaier

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Posts by ryan.hartmaier

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Comment: C: varscan copynumber producing highly variable data
... Yes, sorry I should have included that in my post.  I used --data-ratio to adjust for the difference in sequence coverage.  All other options were default. ...
written 3.2 years ago by ryan.hartmaier0
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varscan copynumber producing highly variable data
... I ran varscan copynumber on my high coverage, whole genome paired end data (matched normal @ 30x & tumor @ 65x after duplicate removal) using default parameters and followed the workflow on the varscan webpage (copynumber, copycaller, DNAcopy segmentation following the R code sample from Chris). ...
varscan copynumber written 3.2 years ago by ryan.hartmaier0 • updated 3.2 years ago by poisonAlien2.4k
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Comment: C: Pindel And Mac Os X
... Hi Kai, I am struggling to get this working. I followed the install instructions and ran ./INSTALL but kept getting a series of fatal errors looking for khash.h opm.h and bam.h. I am running OSX 10.8.3. I installed samtools (v 0.1.19) via homebrew. I also tried uninstalling Xcode like you just s ...
written 4.5 years ago by ryan.hartmaier0
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Comment: C: Bam2Cfg Parameter Description
... Thanks Chris. I'm too focused on my single library bam file - that make sense. ...
written 4.5 years ago by ryan.hartmaier0
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Bam2Cfg Parameter Description
... I've been looking through all the Breakdancer docs for more detailed description of the options in bam2cfg.pl - specifically for what -s represents. The 'minimal mean insert size' seems a little ambiguous. If it was 'minimum insert size' or 'mean insert size' I'd know exactly what it means, but 'm ...
breakdancer written 4.5 years ago by ryan.hartmaier0 • updated 8 months ago by lionair0

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