Resource bundle
The GATK resource bundle is a collection of standard files for working with human sequencing data. We provide several versions of the bundle corresponding to the various reference builds, but be aware...
View ArticleRead groups
There is no formal definition of what is a read group, but in practice, this term refers to a set of reads that were generated from a single run of a sequencing instrument. In the simple case where a...
View ArticleInstall with conda, gatkcondaenv.yml not found
This link from https://software.broadinstitute.org/gatk/documentation/article?id=11049 is dead and no link is present in https://software.broadinstitute.org/gatk/documentation/article?id=12836. Where...
View Articlehow can i get vcf file without repeat snps?
i just call snp with my several samples` RNA-seq data . then i get several vcf files , so i just use the function "MergeVcfs" to combine them into a big vcf files. and i use the...
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What the meaning of this WARN?
Happy Thanksgiving to GATK staff !!! i know you guys are on vacation , so i am no hurry to get answer.but i still want to ask it in advance. here is my question: when i run GenotypeGVCFs , i got a warn...
View ArticleAbout "Ask the team"
This is the place to post any questions, problems or bug reports for the GATK development team to look at. We try to respond within a reasonably short amount of time, but keep in mind that we are not...
View ArticleUse VariantsToTable to extract alternate allele count
I'm using the following VariantsToTable command options to extract fields from a VCF file: /usr/lib/jvm/jre-1.8.0-openjdk/bin/java -Xmx8g -jar /home/1GenomeRef/GATK/GATK_3.5/GenomeAnalysisTK.jar \ -T...
View ArticleJEXL error arising from SNPs with zero coverage for either REF or ALT alleles
I ran: gatk-4.0.11.0/gatk SelectVariants -R Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fasta -V variants/P2-E8-ACTGAGCG-CTTAATAG_S152_first_pass_filtered.vcf -select...
View ArticleVariant Recalibrator Error: Track Input out of Coordinate Order on contig ....
Hi: After running haplotypecaller on SNPs and Indels, I wanted to recalibrate the variant scores using VariantRecalibrator on SNPs and INDels simultaneously. Only 4 samples were used (just testing the...
View ArticleUmiAwareMarkDuplicatesWithMateCigar between Picard 2.9.0 and 2.18.9
Hi, My institution is moving the HPC servers, and as a side effect causes a small downgrade of Picard, from 2.18.9 to 2.9.0. I have followed the release notes and there seems to have no algorithm...
View ArticleHow can I check which version of picard I am running?
Hi, I have used gatk and picard to mark & remove duplicates and indel realignment. I can see the gatk version from commandline. Is there any way to find which version of picard I am running?
View ArticleVariantRecalibrator - Can't do comparison because Locatables' contigs not...
Hi, sorry if the question isn't precise enough. Here's the command: tools/gatk-4.0.11.0/gatk VariantRecalibrator -R data/humanRefGenome/hs37d5.fa \ --variant...
View Articleabout argument presentation
Dear team, I find it sometimes quite non-intuitive which to specify from -<LETTER> <value> <LETTER>=<value> --some_param <value> and/or some_param=<value> with some...
View ArticleGenomicsDBImport terminates after Overlapping contigs found error
My original query was about batching and making intervals for GenomicsDBImport, but I have run into a new problem. I am using version 4.0.7.0 I tried the following: gatk GenomicsDBImport \...
View ArticleIssue with GenotypeGVCFs - GATK 4.0.10.1
Hi, I have got a problem running GenotypeGVCFs. The error is mentioned below. A USER ERROR has occurred: Bad input: malformed RAW_MQ annotation: 2346838272,3678071 Apparently, it seems the issue has...
View ArticleSplitNCigarReads exception
my script : java -jar ~/bin/gatk-3.2-2/GenomeAnalysisTK.jar -T SplitNCigarReads -R Gmax.fa -I NPB18L_mark.bam -o NPB18L_snc.bam -U ALLOW_N_CIGAR_READS -fixNDN when i use -fixNDN, it will be:...
View ArticleVariants with AD 0,0 and DP 0
I was investigating why some of the variants in my vcf produced with HaplotypeCaller miss some fields such as QD, DP, MQ, MQRankSum, BaseQRankSum. I understood why by searching this forum, some of...
View ArticleVariant calling design
This discussion was created from comments split from: New to the forum? Ask your questions here!.
View ArticleMutect2
This discussion was created from comments split from: New to the forum? Ask your questions here!.
View ArticleGATK4 pre-processing
Dear GATK team. Hello. I conducted GATK pre-processing using GATK 4.0.2. I have some questions. I used wxs ngs data for mutation calling. Do you recommend I use exome interval bed when I use...
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