xmzhuo

without the umi option: seems like the tail trimming is not as aggressive. ie with --umi will trim the tail 11bp of read1, GCCACAGATCG; without --umi will only trim the...

Thanks bioXiaoheng, did a sed to replace all space with tab and it work.

I have similar issue. java.lang.StringIndexOutOfBoundsException: String index out of range: -2 at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createAndFilterGencodeFuncotationsByTranscript(GencodeFuncotationFactory.java:281) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:338) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:138) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:113) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.lambda$enqueueAndHandleVariant$0(Funcotator.java:502) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at...

Hg38 On Wed, Mar 31, 2021, 11:51 Jonn Smith ***@***.***> wrote: > @xmzhuo Interesting. Is this hg19 or hg38 > data? I can add this to our tests. > >...

I have similar issue: input is from pyclone vi with WGS data. The cluster table 1 2 3 4 5 10 1805 203 116 1471  #The code I run...