- Last Active
Some updates: The error output is OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00007ff011600000, 2365587456, 0) failed; error='Cannot allocate memory' (errno=12) There is insufficient memory for the Java Runtime Environment to cont…
I found a solution: make a file .cluster.env add PATH=/home/XXX/R-3.0.2/bin:$PATH add following to .bash_profile if [ lsb_release -i|cut -c17-20 == 'Cent' ] ; then source ~/.cluster.env fi
Thanks @Geraldine_VdAuwera !
I am in the same situation: without normal samples for detecting variants. Any advices?
(Quote) Hi @Geraldine_VdAuwera, could you kindly explain a little bit more why HaplotypeCaller on single sample could not be followed by VariantRecalibrator? I didn't found related info in other places. EDIT: I found in FAQ section...
Dear @Geraldine_VdAuwera, Thanks for the guide, just want to be clear: after merge, dedup and realn are recommend, but not recal ? Because recal will use far too much resource, and pay-off is not good?
(Quote) Hi @Geraldine_VdAuwera, thanks, should I assign a new unified @RG for the merged file, or I could leave it as it is, and following snp calling programs will handle different @RG? If I need to change them, any suggestion for the new RG?
Sorry for the ambiguous question, your answers is what I wanted to know. Right now I am using UnifiedGenotyper to find SNV in the whole exome sequencing data. Probably I will select the bad SNPs from the raw output of UnifiedGenotyper basing on fix…
Thanks rpoplin. Assume that I want to supply a false positive sites for GMM, how could I get such dataset from my raw VCF datatset? Do you have any experience on this since there is an option for customized sites?