Closed ZhenyuZ closed 5 years ago
I'm also seeing this happen on a large subset of WGBS samples (perhaps 25%). I'm consistently getting segfaulting in the middle of vcf2bed runs on large pileup.vcf.gz files from the biscuit pipeline. I can provide example files (though they're quite large) if needed.
I think a lot has been updated since last year. Could you provide me the version number of biscuit you are using? Thanks.
I'm using version 0.2.2.20170522, which I see is not the latest release. I'll try the latest version, and I'll report back tomorrow
New version seems to solve the problem - this can be resolved. Thanks!
fwiw, if you use samblaster with biscuit, be absolutely certain to use a version later than 0.3.2
--t
On Wed, Oct 17, 2018 at 10:48 AM Chris Miller notifications@github.com wrote:
New version seems to solve the problem - this can be resolved. Thanks!
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Thank you for getting back @chrisamiller . I am glad it worked!
I followed the instructions to use biscuit 0.2.2.20170522 for alignment and so on using a 58GB TCGA WGBS file. I repeatedly got segmentation fault at vcf2bed step
biscuit vcf2bed -k 10 -t cg output.vcf.gz > output.cg.bed
job killed when the output is about 42Mb. I have tried small input and have no problems.
Btw, I assume I can chunk the input VCF to smaller ones and get the same result after merging the output. Could you confirm this?