picard markdup error:Value was put into PairInfoMap more than once
Hi, all! I get the error information Value was put into PairInfoMap more than once when I use picard to mark duplication. I have already tested the newest version bwa 0.7.16a and picard 2.10.7. My...
View ArticleDoes GATK work with polypolids?
Hi, I would like to use GATK for SNP variant and indel variant calling in wild relatives of a crop plant. I have a good reference genome for the diploid crop where I could map my reads but my species...
View Articlewhat's difference between a read marked by "sam FLAG 1024" and marked by "...
HI, 1 . when I run the following command : "samtools view -h -f 1024 bwa.raw.bam " , then can not get any reads , so I think BWA do not markduplicates to use" FLAG 1024". 2 after I deal with...
View ArticleJoint genotyping of trio exome
I am running genotypeGVCFs for trio exome datasets (Father, Mother, and Child). java -jar GenomeAnalysisTK.jar \ -T GenotypeGVCFs \ -R reference.fasta \ --variant father.g.vcf \ --variant mother.g.vcf...
View ArticleWhat is purpuse of multiple True Sites in VQSR
I have 3 questions: 1- What is the exact purpose of having both HapMap and Omni True Sites in VQSR, vs just one; 2- If I want to restrict the variant calling to my custom list of positions. Which of...
View ArticleGATK 4 VariantRecalibrator throws error for missing R path, but only for SNPs
I'm not using the --rscript_file option, but VariantRecalibrator for SNPs still throws an error for it, but it's fine with the exact same command, except -mG 4, in the INDEL run. And it produces the...
View ArticledbSNP_RS seems to not be annotated with Oncotator 1.9.3
Oncotator 1.9 seems to not be annotating dbSNP annotations (dbSNP_RS), leaving all elements blank in this column. Other annotations are correctly annotated. My command line is oncotator -v --db-dir...
View ArticleHaplotypeCaller raises an error with -A BaseCountsBySample
Hi GATK team , FYI I'm getting the following error with GATK 3.7: <br />java -X -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta --validation_strictness LENIENT -I .bam.list \...
View ArticleGATK 3.8 Dictionary cannot have size zero
Hi, today I wanted to update my pipeline from running on GATK3.6 to 3.8. But now it complains about the dictionary. ERROR -- ERROR stack trace java.lang.IllegalArgumentException: Dictionary cannot have...
View ArticleGATK 3.8 logger ERROR
Hi, after updating to GATK 3.8 I found the following ERROR in my log file. ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:f...
View Articlewhat's the point of Co-realign in indel realignment?
i have an question about Co-realign,hoping someone to solve it,and thanks for that! question: with gatk RealignerTargetCreator input is a list of normal-tumor bam files,is there any difference of...
View Article[GATK4-BETA3]BwaAndMarkDuplicatesPipelineSpark command line problems
I use GATK4-BETA3 in X86 system and run the pipeline BwaAndMarkDuplicatesPipelineSpark,and have several problems,but the other spark pipeline can use correct, I doubt that whether the code of...
View ArticleProblem with joint genotyping
Dear Team, I am running joint calling (according to Best Practices). I have ~800 samples from 3 different centres.First I run CombineGVCFs on cases from batch1(~130samples), controls from...
View ArticleGATK VQSR on indels
Hi Are there any precautions to be taken before applying VQSR to an "INDEL" VCF? meaning, how does the algorithm inside VQSR recognize whether an indel in the input VCF is the same as in the training...
View ArticleGenotype Given Alleles mode
Can a multi-sample VCF with multiple genotype columns, 1 column per sample be used as the --alleles file in GGA, so that the prgram is given a choice of various alternate alleles to consider for each...
View ArticleSNV gets dbSNP annotation in one sample, doesn't get annotated in another one
Hello everyone, I recently run HaplotypeCaller for GATK3.7 on a series of samples (several GATK runs performed at the same time), using the latest release of dbSNP(150). This was the command line I...
View ArticleFastaAlternateReferenceMaker for polyploid
Are there any tools similar to FastaAlternateReferenceMaker that can create fasta sequences from a pooled-sequencing vcf file? The sample data came from 25 pooled diploid individuals, so I created the...
View ArticleLocation of documentation for option types
Hi, Could you provide a pointer to the place in the documentation where types such as RodBinding[VariantContext] ArrayList[String] List[Type] Set[File] etc and their exact usage are described? Despite...
View ArticleQuestions about datasets for benchmarking
This discussion was created from comments split from: Which datasets should I use for reviewing or benchmarking purposes?.
View Article(howto) Revert a BAM file to FastQ format
NOTE: This tutorial has been replaced by a more recent and much improved version, Tutorial#6484. Objective Revert a BAM file back to FastQ. This comes in handy when you receive data that has been...
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