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dnaase / Bis-tools

A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )
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Can't find BisulfiteCountVariant Walker #1

Open massfl opened 6 years ago

massfl commented 6 years ago

Hello,

I ran Bis-SNP1.0.0 from he prompt line using the following command: (Java version: JDK8) java -Xmx10g -jar BisSNP-1.0.0.jar \ -R mm10.fa \ -I file.bam \ -T BisulfiteCountCovariates \ -knownSites dbSNP-150.vcf \ -cov ReadGroupCovariate \ -cov QualityScoreCovariate \ -cov CycleCovariate \ -recalFile File.csv

and got the following result: ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef): ERROR ERROR This means that one or more arguments or inputs in your command are incorrect. ERROR The error message below tells you what is the problem. ERROR ERROR If the problem is an invalid argument, please check the online documentation guide ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool. ERROR ERROR Visit our website and forum for extensive documentation and answers to ERROR commonly asked questions https://software.broadinstitute.org/gatk ERROR ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself. ERROR ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: BisulfiteCountCovariates ERROR

I can't find the BisulfiteCountCovariate.java walker in BisSNP files could that at least part of the probelm?

Thanks for helping

decodebiology commented 6 years ago

I am having same issue. Please help.

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: BisulfiteCountCovariates
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: BisulfiteTableRecalibration
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: BisulfiteCountCovariates
##### ERROR ------------------------------------------------------------------------------------------
massfl commented 6 years ago

Hi Gridhrahakshi No answer form dnaase, I was wondering if you found a solution to the problem? Thanks

decodebiology commented 6 years ago

Hi massfl, I started using BS-SNPer, that serves my purpose.

https://github.com/hellbelly/BS-Snper

Also the developer of the tool is superfast in responding to the queries.

Developer’s contact: Shengjie Gao gaoshengjie@genomics.cn

massfl commented 6 years ago

Great, thanks for the idea, I'll give it a try

thakki commented 6 years ago

Can you please add BisulfiteCountCovariates?

insectopalo commented 5 years ago

Hei @decodebiology do you know if BS-Snper accepts Bismark bam files as input?

decodebiology commented 5 years ago

Hi @insectopalo , yes it accepts Bismark aligned sorted and indexed BAM files as input.

bartgrantham commented 5 years ago

Is there any response on this issue? It's referred to in the manual, as well as in bissnp_easy_usage.pl. Is this software abandoned?

katwre commented 5 years ago

Hi, I have similar problem. This tool doesnt see BisulfiteRealignerTargetCreator.

ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: BisulfiteRealignerTargetCreator
decodebiology commented 5 years ago

Hi, Unfortunately, it looks like the authors don't maintain this tool anymore. Have a look at above mentioned BS-SNPer tool and check if it helps.

FleurGaBru commented 3 years ago

I had the same issue with the newest bis-snp release and think, that I got it to work. What is important to mention is, that the worker names are defined by the current version of GATK. As bis-snp 1.0 uses GATK 3, I checked the archived documentations here. The recalibration step is very well explained here.

This resulted in the following working code for the human example data, when bis-snp was installed with conda:

1) Analyze patterns of covariation in the sequence dataset

bis-snp -R hg18_unmasked.plusContam.fa -I normalMerge_chr11-7M-9M.nodups.withhead.bam -T BaseRecalibrator -knownSites dbsnp_135.hg18.sort.vcf -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -o recalFile_before.csv

2) Do a second pass to analyze covariation remaining after recalibration

bis-snp -T BaseRecalibrator -R hg18_unmasked.plusContam.fa -I normalMerge_chr11-7M-9M.nodups.withhead.bam -knownSites dbsnp_135.hg18.sort.vcf -BQSR recalFile_before.csv -o post_recal_data.table

3) Generate before/after plots

bis-snp -T AnalyzeCovariates -R hg18_unmasked.plusContam.fa -before recalFile_before.csv -after post_recal_data.table -plots recalibration_plots.pdf

4) Apply the recalibration to your sequence data

bis-snp -T PrintReads -R hg18_unmasked.plusContam.fa -I normalMerge_chr11-7M-9M.nodups.withhead.bam -BQSR recalFile_before.csv -o normalMerge_chr11-7M-9M.nodups.withhead.recal.bam

Hopefully this information will be useful :)

weishwu commented 3 years ago

@FleurGaBru Thanks for posting your solution. My concern, however, is that BaseRecalibrator is blind to the C->T bisulfite conversion. The default behavior of GATK recalibration is to assume all mismatches are sequencing errors, with the true SNP sites masked by a known SNP vcf. Bisulfite treatment causes all unmethylated Cs to be converted to Ts, which, if not masked out, will substantially bias the recalibration. This is why the bis-SNP author developed BisulfiteCountCovariates to do recalibration instead of using GATK's BaseRecalibrator, based on my understanding. It's unfortunate that the author seems to have abandoned the maintenance while the community is still viewing bis-SNP as one of the best SNP callers for bis-seq data.

AliaMW commented 3 years ago

Hello! I am trying to run an analysis of paired-end bisulfite data using BS-SNPer. The issue I have is that I am quite new and I just have as a reference for the SNP calling a book chapter providing instructions on how to call SNPs in bisulfite data using BisSNP. As far as I've understood, BS-SNPer does not have as many intermediate steps as BisSNP therefore I need to just provide a reference genome, the input .bam files for my paired-end reads and tweak the parameters to obtain a .vcf?

Is there anyone who can confirm or deny this?

Also, I was told by my supervisor that it'd be a good idea to use .bed files but I am not sure if I could use this as a reference instead of a whole genome file. If I understood correctly, this should be possible. Again, if anyone had any idea or could shed some light on this, it'd be of great help. Thanks!