User: R.A.

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R.A.50
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Posts by R.A.

<prev • 32 results • page 1 of 4 • next >
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Problem in installing mclust package R
... 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 ...
R lgfortran mclust written 12 days ago by R.A.50 • updated 12 days ago by Jean-Karim Heriche17k
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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
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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 WouterDeCoster35k
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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 WouterDeCoster35k
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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
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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
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Comment: C: How to merge vcf files (output of VarScan2 somatic)?
... 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
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Problem in using picard.jar
... 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 ...
picard written 4 weeks ago by R.A.50 • updated 4 weeks ago by Pierre Lindenbaum116k
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Comment: C: How to merge vcf files (output of VarScan2 somatic)?
... 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
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How to merge vcf files (output of VarScan2 somatic)?
... 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 ...
vcf indel merge varscan2 snp written 4 weeks ago by R.A.50

Latest awards to R.A.

Student 9 weeks ago, asked a question with at least 3 up-votes. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 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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