convert illumina manifest to csv

Is this tool no longer available: BpmToNormalizationManifestCsv

java -jar picard.jar BpmToNormalizationManifestCsv \
  INPUT=input.bpm \
  CLUSTER_FILE=clusterfile.egt \
  OUTPUT=out.csv

'BpmToNormalizationManifestCsv' is not a valid command. See PicardCommandLine -h for more information.

Is there another tool that will convert a manifest to csv? Thank you :).

illumina

• 1,299 views • link

updated 3.3 years ago by rpolicastro

• written 3.3 years ago by bioguy24

1 answer

What version of picard are you running? As of the latest version (3.0.0) that program is present.

• 0 views • link

written 3.3 years ago by rpolicastro

I will update to 3.0.0, thank you :).

• 0 views • link

written 3.3 years ago by bioguy24

More posts like this

VCF files
written 2.0 years ago by Sanazarghami4444 •

Hello, I run this code for produce VCF files of samples that i work on it : ``` java -jar picard.jar MarkDuplicates \ INPUT=/home/zr/SRR3229050/SRR3229050_sorted.bam \ …
Picard MarkedDuplicates Error: Unable to access jarfile picard.jar
written 4.5 years ago by connorjfausto •

Hello, I am trying to run MarkedDuplicates on Picard, but it says that it cannot open the java file. My initial code is: java -jar …
Running a tools depending on old version of Picard that cause problem
written 6.9 years ago by Alexso •

Hello, I’m trying to make the following tool run (http://www.appliedbioinformatics.com.au/index.php/SGSGeneLoss), but I cant suceed… I think that the problem come from an old version of …
ATAC-Seq trimming reads to 36bp
written 7.0 years ago by Bioinfo_2006

I have ATAC-Seq data of 75bp length mapped using bowtie 2, and I had posted earlier (https://www.biostars.org/p/387531/) because I had the issue of flipped reads. …
Problems running variant calling (VC) GATK: SAM/BAM/CRAM file dedup.bam is malformed
written 7.9 years ago by Lila M

Hi everybody, I'm trying to carry out some VC analysis, but I'm not very advanced at it, so I am a bit struggle... For my …
using bash variable in picard MarkDuplicates command
written 8.0 years ago by bioguy24

In the below `bash` the two variables `$bname` and `$sample` are extracted correctly however when I pass them to the `java` command `$bname` is set …
sortsam (picard) error in identifyting samfile
written 8.1 years ago by shuksi1984 •

What does SAMFormatException mean? How to troubleshoot this error. I got following error: > Exception in thread "main" htsjdk.samtools.SAMFormatException: Error > parsing text SAM file. …
Picard: Value was put into PairInfoMap more than once. Even bwa enabled -M
written 9.4 years ago by pentiumy •

I try to follow this link(GDC protocol of processing TCGA data) https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#dna-seq-alignment-command-line-parameters to process some cancer exome sequencing file. I used TCGA bam file as …
What parameters to set in SNPEff to improve annotation results from the Pilon VCF input to SNPEff?
written 9.5 years ago by human_genomeXXX •

I run the code line: java -Xmx10G -jar snpEff.jar -c snpEff.config -s SNPEffOutputStats.html -v -no-downstream -no-upstream m_tuberculosis_H37Rv pilon_output.pilon.vcf > SNPEffSampleGenome_merge.var.ann.vcf And it produces results, but …
picard error version 1.139 on ubuntu 14.04
written 10.8 years ago by bioguy24

I seem to have trouble with calling picard from the command line but other tools work perfectly. path: <pre> /home/cmccabe/Desktop/NGS/bedops-2.14.4/bin:/home/cmccabe/Desktop/NGS/samtools-1.2:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/cmccabe/Desktop/NGS/bedtools2-25.0/bin:/home/cmccabe/Desktop/NGS/bbmap-35.59:/home/cmccabe/Desktop/NGS/FastQC-0.11.4:/home/cmccabe/Desktop/NGS/picard-tools-1.139</pre> The code …