GenotypeGVCFs on pooled data sets fail for ploidy > 10
Hi, I'm currently analysing a data set of six pools, 25 individuals in each (ploidy 50), of a non-model organism. I initially ran HaplotypeCaller with parameter -ERC GVCF and then attempted to do joint...
View ArticleSNP and INDEL VariantFiltration Parameters
Hi, I've been looking for recommended filter expressions for SNP and INDEL variant filtration. I found these articles on the topic: one and two. I noticed that in the second article the SOR annotation...
View ArticleGATK 3.7 HaplotypeCaller
Hi, I've been looking at the release notes for GATK 3.7. I would like to know if turning on the -newQual setting for HaplotypeCaller would be considered Best Practice for WGS and WES pipelines. Thanks,...
View ArticleHow to get rid of false positives? And troubles with VQSR
For the last couple of months we have been trying to analyze an exome data set of ~1500 samples. Within the data there are 2 sets, ~1200 control samples sequenced at one site, and ~300 cases samples...
View Articlewhere do I find SamToFastq.jar ? [reproducibility?]
Dear Community, I am from system-administrator side, and totally new in this field about bio-informatic, so excuse my weird question. I am attempting to reproduce results of: Nature Biotechnology 33,...
View ArticleCombineVariants - duplicate reads are generated for the same chr:pos
I am merging two VCFs. the records are as below VCF1: CHROM POS ID REF ALT QUAL 1 1247578 . TG TGG,TGGG,TGGGG,TGGGGG,T,TGGGGGG 53367.32 VCF2: CHROM POS ID REF ALT QUAL 1 1247578 . TG...
View Articlepicard tools FilterSamReads
Hi I am trying to extract reads from a Read list file from a bam file using the command using FilterSamReads option. At first I got the "SAM validation error: ERROR: Record 174124896, Read name...
View ArticleConference proceedings: Sheila's experience at AGBT 2017
As part of our job providing support to the GATK user community, our team takes turns traveling to conferences, both to learn what's going on in the field at large and to advertise the latest features...
View Articlemutect2 FFPE filter
Hi, Does mutect2 implement the "Phred scaled Q-score for FFPE artifacts" described here http://genomics.broadinstitute.org/data-sheets/error-proofing-exome-sequencing-somatic-variant.pdf
View ArticleClik here to view.
Support team appreciation day -- say hi and get a prize
I want to give mad props to my team. Every day they handle new questions about obscure error messages or unusual experimental designs, on top of their ongoing efforts to develop new documentation...
View ArticleWhich training sets / arguments should I use for running VQSR?
This document describes the resource datasets and arguments that we recommend for use in the two steps of VQSR (i.e. the successive application of VariantRecalibrator and ApplyRecalibration), based on...
View ArticleRuntime Error, SRA Accession problem.
Hello. My DepthOfCoverage returns RUNTIME ERROR, which is strange, because exactly the same command worked perfectly yesterday. Seems like I'm having a problem with automatic downloading of SRA toolkit...
View ArticleHelp me understand why this variant was called
This variant was called with MuTect2 T/N mode : chr7 152008861 . A T . PASS \ ECNT=1;HCNT=70;MAX_ED=.;MIN_ED=.;NLOD=96.12;TLOD=37.01 \ GT:AD:AF:ALT_F1R2:ALT_F2R1:DP:FOXOG:QSS:REF_F1R2:REF_F2R1:SAC \...
View ArticleEmpty vcf when generating PON with MuTect2
Hi, First, sorry if it's a duplicate question. I have looked for solution, but didn't find. I have 8 exomes data from 4 patient: normal and tumor. I ran MuTect2 (in GTAK 3.7) in normal/tumor mode, and...
View ArticleShould I use sorted.bam or clean_dedup_recalibrated.bam for getting the...
Recently we performed exome sequencing using Nextera Illumina platform for three samples (Father, Mother and Son). This time we used the new kit for exome sequencing. I am trying to collect the...
View Articlev3.7-0-gcfedb67: -T RealignerTargetCreator does not support --known blah.vcf.gz
Hi, it seems GATK does not relaize that it has opened a vcf.gz (actually vcf.bgz file). java -Djavaio.tmpdir=. -jar /scratch/mmokrejs/GATK/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T...
View ArticleI have 50 exome samples belong to 25 families. Do I run GenotypeVCFs on...
We have exome sequenced data for 50 samples in total for a cardiac disease. But they have been sequenced in different batches. Even some of the batches were 2 years old. We have relationship...
View ArticleShould I provide the exome target list (-L argu) even while calling gVCF file...
Hi, Recently we performed exome sequencing using Nextera Illumina platform for three samples (Father, Mother and Son). I downloaded the exome interval list from Illumina's website. 1) Trimmed the raw...
View ArticleGATK 3.7 error message: not a strict subset of per read allele map alleles
I am trying to run GATK 3.7 for variant calling and I keep getting this error. Any comments about what this error is? Thanks! ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67): ERROR...
View ArticleMap Duplicates invalid link
https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS&p=1 This link is missing http://gatkforums.broadinstitute.org/gatk/discussion/2799/howto-map-and-mark-duplicates
View Article