What causes BaseRecalibratorSpark to run for a long time and end up failing...
Hi, GATK team, I am testing BaseRecalibrator in GATK 4.5 beta, when running in LOCAL mode, it finishes pretty fast. However when i run BaseRecalibratorSpark in SPARK mode, it runs for a long time and...
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VQSR: low TiTv
Hi I'm trying out VQSR on a batch of 16 human whole genomes (~25-30x). I was wondering if someone could review the below profiles. It seems the false-positive rate is much higher than the GATK...
View Articlebam files header
Hi, I am new in gatk, and as bioinformatician too I am trying to analyze some public bam files; it included all the genome but I am only interested in plastome genomes. I need to obtain variants from...
View ArticleAre you going to have a working version in few time of the complete GATK Best...
I am trying to use your Spark commands in GATK 4 release in order to execute the GATK Best Practices with Spark and it looks working fine until the BQSRPipelineSpark (I am using...
View Article(howto) Recalibrate variant quality scores = run VQSR
Objective Recalibrate variant quality scores and produce a callset filtered for the desired levels of sensitivity and specificity. Prerequisites TBD Caveats This document provides a typical usage...
View ArticleMergeBamAlignment help
Hi all, I am attempting to go through the Dropseq pipeline, but I have changed a few things to the default. I have aligned my fastq files to the hg38 genome rather than hg19 and I've also used TopHat...
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View Articlepicard ./gradlew shadowJar install error
I have an error when tried to install picard on our system. I am running centOS system. Could you please let me know what should I do? Thank you. [root@NGS:picard]# java -version java version...
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why HaplotypeCaller did not call variants with high alt allele coverage
Hi GATK team, HC variant calling command: GenomeAnalysisTK-3.6.jar -T HaplotypeCaller --dontUseSoftClippedBases -mbq 10 -stand_call_conf 10 -dt NONE -R hs37d5.fa -I UM1.recal.bam -L test.bed -D...
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VariantRecalibrator ERROR: Bad input: Found annotations with zero variance....
Hello GATK Team, Below is the the partial pipeline of my code and I have ** the VariantRecalibrator tool line where I am getting the error: os.system('java -Xmx40g -Djava.io.tmpdir=/Users/seyfim/tmp...
View ArticleMutect1 -> depth of 'PASS' variants
Hi, I have used Mutect1 (tumor-control) for calling variants. As mentioned here: http://archive.broadinstitute.org/cancer/cga/mutect ; that "We currently use cutoffs of at least 14 reads in the tumor...
View ArticlePersistent memory problem with BaseRecalibrator.
I'm using BaseRecalibrator as part of the GATK best practices workflow. My workflow up to this point is trim --> align --> deduplicate --> fix mates. I'm calling BaseRecalibrator like this...
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Haplotype caller not picking up variants for HiSeq Runs
Hello, We were sequencing all our data in HiSeq and now moved to nextseq. We have sequenced the same batch of samples on both the sequencers. Both are processed using the same pipeline/parameters. What...
View ArticleProblem with allele specific annotation AS_QualByDepth (AS_QD) during variant...
Hi GATK team, First a big thank you for all your hard work in developing the tool and supporting the users! I am trying out the allelic specific(AS) annotations in version 3.6. While I have gotten a...
View ArticleBest practice on SRA data
Dear all, I'm trying to detect variants starting from the data on a few (5) SRA files downloaded from NCBI (whole genome resequencing on Illumina GA). I do not have information about lanes (each SRA...
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VariantRecalibrator ERROR: Bad input: Found annotations with zero variance....
Hello GATK Team, I am using the best practices for germline SNPs and Indels in Whole Genomes and Exomes Below is the the partial pipeline of my code and I have ** the VariantRecalibrator tool line...
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Errors in SAM/BAM files can be diagnosed with ValidateSamFile
The problem You're trying to run a GATK or Picard tool that operates on a SAM or BAM file, and getting some cryptic error that doesn't clearly tell you what's wrong. Bits of the stack trace (the pile...
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GATK4 is completely open source
This is one of two posts announcing the imminent beta release of GATK4; for a technical description of features, see this other post. "Wait, what?" Yes, you read that right, we're moving GATK4 to a...
View ArticleVersion highlights for GATK version 3.8
One more 3.x version, for the road! That's right, even as we're ramping up our efforts on GATK4 (we're three beta releases in at this point, and getting down to brass tacks writing the migration guide...
View ArticleAllele-specific annotation and filtering
Introduction and FAQs The current recalibration paradigm evaluates each position, and passes or filters all alleles at that position, regardless of how many alternate alleles occur there. This has...
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