User: R.A.
R.A. • 50
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Posts by R.A.
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2
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... Hello,
I tried to install mclust package R in RStudio using different ways
install.packages("mclust")
devtools::install_github("cran/mclust")
biocLite('mclust')
but I get this error:
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD ...
written 12 days ago by
R.A. • 50
• updated
12 days ago by
Jean-Karim Heriche ♦ 17k
0
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1
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177
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1
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Comment:
C: Problem in using picard.jar
... Oops, my bad. So sorry.
I ran this command: `java -jar picard.jar UpdateVcfSequenceDictionary I=Germline.hc.fpfilterPassed.vcf O=Germline.hc.fpfilterPassed_new.vcf SEQUENCE_DICTIONARY=hg38.fa.dict`
and now everything is fine :-)
Many thanks! ...
written 4 weeks ago by
R.A. • 50
0
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Comment:
C: Problem in using picard.jar
... Dear fin and Pierre, many thanks for your help!
Now I have hg38.fa.dict file :-) However, when I run this command: `java -jar picard.jar VcfFormatConverter I=Germline.hc.fpfilterPassed.vcf O=Germline.hc.fpfilterPassed.bcf REQUIRE_INDEX=true`
to update my vcf file with the new sequence dictionary, I ...
written 4 weeks ago by
R.A. • 50
• updated
4 weeks ago by
WouterDeCoster ♦ 35k
0
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177
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Comment:
C: Problem in using picard.jar
... Dear Pierre, thanks for reply. I downloaded your machine and put all the files in the same directory and ran your command: `java -jar picard.jar MergeVcfs I=Germline.hc.fpfilterPassed.vcf.gz I=Somatic.hc.fpfilterPassed.vcf.gz O=out.vcf.gz`
It returned nothing and gave this exception:
> Exceptio ...
written 4 weeks ago by
R.A. • 50
• updated
4 weeks ago by
WouterDeCoster ♦ 35k
0
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1
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177
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Comment:
C: Problem in using picard.jar
... Hello WouterDeCoster,
No, it doesn't. ...
written 4 weeks ago by
R.A. • 50
0
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1
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177
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1
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Comment:
C: Problem in using picard.jar
... I'm using the latest version of picard: 2.18.20
This are the tools which I try to run by picard, but failed:
NormalizeFasta
MarkDuplicates
MergeVcfs
CreateSequenceDictionary
I'm doing the exact command given from the website.
for example for MergVcfs, this is the command:
java -jar picard.j ...
written 4 weeks ago by
R.A. • 50
0
votes
1
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199
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1
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... Thank you fin swimmer.
Yes it produced an output but just headers are there no more.
Edit:
Sorry I made a mistake. It produces nothing. I mean after getting that notice, I get no outputs. ...
written 4 weeks ago by
R.A. • 50
8
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1
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177
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1
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... Hello every one,
It's about a month that I stuck with picard. Every command that I try to run with picard failed.
And for all of them I get the same error:
> ERROR: Invalid argument '-I' , '-O'
When I try this argument I= or R=
I get this:
> NOTE: Picard's command line syntax is ...
written 4 weeks ago by
R.A. • 50
• updated
4 weeks ago by
Pierre Lindenbaum ♦ 116k
0
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1
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199
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... many thanks for your reply.
This is my command:
java -jar GenomeAnalysisTK.jar -T CombineVariants -R hg38.fa --variant Germline.hc.fpfilterPassed.vcf --variant Somatic.hc.fpfilterPassed.vcf -o output.vcf -genotypeMergeOptions UNIQUIFY
And this is the error when I am using CombineVariants:
& ...
written 4 weeks ago by
R.A. • 50
7
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1
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199
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1
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... Hello,
I have WES data of tumor samples with matched ones extracted from 13 patients (paired-end, illumina). I used BWA mem to align them against hg38, and used VarScan2 to call somatic variations. Now I have 6 files (fpfilter_Passed.vcf) for each patient (Somatic, LOH, Germline for each of snp and ...
written 4 weeks ago by
R.A. • 50
Latest awards to R.A.
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asked a question with at least 3 up-votes.
For Why some probes have "NA" for gene symbol and Entrez ID?
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12 months ago,
created a question with more than 1,000 views.
For Why some probes have "NA" for gene symbol and Entrez ID?
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