Louis Bergelson
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Activity overview
Latest activity by Louis Bergelson-
Louis Bergelson commented,
Hi Andrew E. I think I gave some bad advice about setting -Xmx because I didn't fully understand the question. I've roped in a PathSeq developer who might know what to do in this case.
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Louis Bergelson commented,
Hi Terry, A few questions. What are you seeing change exactly? Is it the result of calling toString() on the genotype context? There's a weird quirk of genotype contexts where they lazily parse ...
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Louis Bergelson commented,
There's a longstanding (and frankly stupid) issue with htsjdk reading samtools queryname sorted files. Htslib and htsjdk disagree about what it means to coordinate sort files. Htslib uses a sort ...
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Louis Bergelson commented,
I would really recommend you install the newest version of GATK if you can. In general 4.1.0.0 should be ok, but it has a bug in FastaAlternateReferenceMaker which wasn't fixed until 4.1.5.0. (I ...
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Louis Bergelson commented,
Hi Luca Stefanucci, This was a known bug in version 4.1.0.0. It's been fixed in recent versions. Please upgrade and try with 4.1.8.0.
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Louis Bergelson commented,
danilovkiri Bhanu Gandham Thank you for providing the test file. We used it to identify and fix a critical performance bug. In the next GATK release your command will run 3 orders of magnitude fa...
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Louis Bergelson commented,
To second danilovkiri, linux is pretty much an essential skill for doing bioinformatics. The good news is that it's actually pretty easy to get started now a days! It used to be hard and scary to...
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Louis Bergelson commented,
You can use the gatk tool PrintReads to select regions of a bam. ``` gatk PrintReads --input original.bam -L Y --output yOnly.bam ```
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Louis Bergelson commented,
Maybe we should have a readme file for all the public data folders that describe what the files are?
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Louis Bergelson commented,
Nickier Targets are the regions the exome capture is aiming to cover . Baits are the positions of the actual bait sequences that are used in the exome capture process. So targets are a region o...