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• Known SNPs for rice for Base recalibration using GATK
  Hi, I am analyzing rice samples for SNP detection using GATK, and for the base recalibration, I ...
• Reference Index and Feature Index not matching while using BaseRecalibrator
  I have downloaded the databases for dbSNP and COSMIC in order to use the BaseRecalibrator tool in...
• GATK4, BaseRecalibrator, Known site, Drosophila
  Hello I study a GATK4 - BaseRecalibrator and I use the drosophila sequence for practice. I didn...
• The Methods To Determine Mads-Box Gene Families In A Newly Sequenced Genome? I Need The Information About The Gene Family Sequence Of Dna, Cdna, Location On Chrommone,Motif?
  We have sequenced a wild rice genome. However, we can not used it for our research by bioinformat...
• Error in GATK BaseRecalibrator arguments
  I tried to recalibrate the bases of my complete genome assembly, but it gave the following error:...
• BaseRecalibrator takes forever to run. Any suggestions?
  Hello, I am trying to run BaseRecalibrator tool from GATK package and it takes forever (more than...
• How to use MSU7 rice genome as reference as there has fasta file format.
  I am working with Whole-genome sequence analysis. I have to use the MSU7 rice genome as a referen...
• GATK quality recalibration to get recalibrated BAM files before SNP calling
  I'm having problems with **quality score recalibration** using **GATK** as most tutorials/example...
• fasta q files or BAM files of RNA seq Oryza sativa(rice)
  hey I want to know where i can find the fasta q files or BAM files of RNA seq Oryza sativa(rice)...
• Is there any resources for identifying human to rice orthologs?
  I know the resources for finding plant to plant orthologs databases and resources like Genevestig...
• Facing trouble to analyze the different Rice genes on David Bioinformatics Resources 6.8
  Hi, I am dealing with Rice for RNA-Seq analysis. Nowadays, I am facing an issue at David bioinfor...
• GATK BaseRecalibrator Step
  Hello I have been struggling with GATK 4 and feeling an acute lack of the command line pipelines...
• How To Link To Gbrowse And Load Custom Track From External Data
  I am implementing a web frontend for a tool I've developed for annotating a particular type of ge...
• is the output.table correct after BQSR?
  Hi， after I ran the BQSR command gatk --java-options "-Xmx4G" BaseRecalibrator -R /home/ri...
• error using bqsr and incompatible contigs
  Using the below command in GATK 4.0.6.0, I am getting: A USER ERROR has occurred: Input file...
• How to read the GATK BaseRecalibration report
  Hi everyone, I use GATK to do SNP call.But the BaseRecalibration report confused me. what is  re...
• baserecalibrator error: Unable to find color space information in SOLiD read
  When running GATK baserecalibrator on SOLiD read data, I initially obtained the following error: ...
• How to include each steps in the bam header
  Hi , Im doing sequence analysis (starting from alignment of fastq to BaseRecalibrator). I would ...
• GATK --ploidy
  When I use GATK to conduct SNP detection, I have seen that the default value of 'GATK -ploidy' is...
• How to apply GATK on mtDNA sequencing data?
  Hello, everyone. I sat up a mtDNA pipeline using `samtools mpileup` + `varscan2` to do variant ca...
• How To Locate A Homolog Gene On A Newly Sequenced Genome (For Example A Wild Rice Genome)? Thank You For Help?
  We have sequenced a wild rice genome. However, the data is just a lot nucleic acid date for us. W...