How can I prepare a FASTA file to use as reference?
This article describes the steps necessary to prepare your reference file (if it's not one that you got from us). As a complement to this article, see the relevant tutorial. Why these steps are...
View ArticleOverlapping SNV and deletion
Hello, I've recently encountered a situation in which a SNV overlaps a single base pair deletion variant. The output from GATK v3.6 HaplotypeCaller is as follows: 8 145738767 . CG C 7919.73 ....
View ArticlePGT/PID fields Mutect2
Hello! I am using Mutect2 as variant caller for whole exome sequencing tumor/normal sample pairs data. I have seen that sometimes (not often) the mutation sites presented the PGT/PID fields. For...
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HaplotypeCaller missing SNP calls
Hi I am in the process of validating the HaplotypeCaller in gatk3.8, and it is missing some obvious SNPs in GRCh37. Playing around with various parameters I can make the variant being called or not....
View ArticleA fatal error has been detected by the Java Runtime Environment
Hi, Since a few days GATK crashes at PrintReads with a fatal java error. We tried GATK 3.7 and 3.8; OpenJDK 1.8.0_144, Oracle JDK 1.8.0_102, OracleJRE 1.8.0_144 and 1.8.0_102 and we always get the same...
View ArticleTrying to gather InsertSizeMetrics from the .bam file but getting an error.
[Mon Oct 02 18:12:59 GMT 2017] CollectInsertSizeMetrics HISTOGRAM_FILE=insert_size_histogram.pdf INPUT=input.bam OUTPUT=output_insert_size_metrics.txt DEVIATIONS=10.0 MINIMUM_PCT=0.05...
View ArticleMixed PoN (Blood + FFPE) ?
Hi, I have some FFPE WGS data. I am able to access TCGA bam file. I want to build a PoN for mutation and CNA analysis with 900+ blood tissues (TCGA) and 30+ FFPE tissues (TCGA + my own). Does this PoN...
View ArticleSplitNCigarReads results in all reads failing MalformedReadFilter?
Hi, I'm following the GATK best Practices workflow for SNP and indel calling on my RNAseq data, I'm currently at the "Split'N'Trim and reassign mapping qualities" step but come across some problems,...
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(How to) Run FlagStatSpark on a cloud Spark cluster
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section. It may take a minute or a...
View ArticleHC listing depth one read less
Hi, I ran haplotypecaller on a bunch of samples using the following commands: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -drf DuplicateRead -R hg19.fa -I SAMPLE.bam -o SAMPLE.g.vcf -L...
View ArticleFastaAlternateReferenceMaker gives the input sequence back without applying...
Dear all, I have sequencing reads (mapped with tophat/bowtie2 to reference genome) and from those created vcf files using samtools. Now I have tried to get the fasta nucleotide sequence of a certain...
View ArticleHow to generate BAM file (from fastq files (Paired-end)) compatible with...
I have two fastq files (first and second reads in paired end data in separate .fastq files). I want to convert them to BAM file so that I can use the Picard Tool CollectInsertSizeMetrics. However, I am...
View ArticleGATK runtime error (READ_MAX_LENGTH must be > 0 but got 0) with 1000g bam
Hi, I'm trying to build a pon with GATK 3.7-0 to use with mutect2. For that, I've downloaded 80 exome bam files from the 1000g project (GBR, TSI, IBS and CEU populations). For most of them, when I try...
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DP differences between haploid and diploid mode
I would appreciate some help in understanding better the differences between haploid and diploid mode when it comes to calling and joint-genotyping (HaplotypeCaller + GenotypeGVCFs) in gatk. In...
View ArticleCrashes with segmentation fault in shipped `libVectorLoglessPairHMM.so`
Dear GATK people, Our scientists reported, that GATK 3.6 and 3.7 terminates with a segmentation fault on a lot of Intel systems. Crazily enough, it’s not reproducible on all of them despite being the...
View ArticleWhich one should I use for ContEst --popFile?
http://gatkforums.broadinstitute.org/gatk/discussion/6687/how-to-build-get-populationallelefrequencies-vcf-for-contest says I should use...
View ArticleWhat's in the resource bundle and how can I get it?
NOTE: we recently made some changes to the bundle on the FTP server; see the Resource Bundle page for details. In a nutshell: minor directory structure changes, and Hg38 bundle now mirrors the cloud...
View ArticleIllegal argument exception when running HaplotypeCaller
Hello, One of my jobs is consistently failing to run HaplotypeCaller with the following error message: ERROR ------------------------------------------------------------------------------------------...
View ArticleVariantAnnotator issue with trios!
Hi, First I have to express my appreciation for great tools and the support we are getting from The Broad Institute on this forum. Following BestPractices, I ran the VariantAnnotator walker on GATK 3.8...
View ArticleInvalid command line: Malformed walker argument
Hi! tried running my pipeline with a most current nightly version of GATK and the walker seems to be broken: gatk -T RealignerTargetCreator -R test.bam -nt 6 -o test.intervals Got the following error:...
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