MuTect2 LOD calculations
I am interested in how NLOD and TLOD are calculated in MuTect2. The MuTect2.java code...
View ArticleSVDiscovery error with X chromosome
Dear GenomSTRIP team, I am using GenomSTRIP to detect deletions in goat. I could successfully run the pipeline (SVpreprocess, SVdiscovery, and SVgenotyping) on all autosomes but the SVdiscovery script...
View ArticleWhen should I use dToxoG?
We are running MuTect2 and would like to correct for oxidation artifacts with dToxoG. Is there a best practice on when I should run this program? I have collected Picard CollectOxoQMetrics by read...
View ArticleMuTect2 and Alternate Allele Calls
Hi there, We have a few calls in our dataset that are slightly confusing. We are getting a triallelic flag, which is expected, but only getting one alternate allele outputted to the VCF. The alternate...
View Article3.5 -> 3.6 regression in VariantFiltration Genotype filter?
I am trying to run VariantFiltration using a genotype filter on DP. This works in 3.5; however, with 3.6 it throws a rather uninformative error (stacktrace below). The command is something like: java...
View ArticleMuTect2 and multiple read groups per sample, issue with index
I have an issue with BAM files containing multiple read groups for the same sample (identical SM:), essentially this is the same situation as my MuTect1 related question form 2 years ago:...
View ArticleGenotypeGVCFs ERROR
Hi all, I meet some error while generate vcf files with GenotypeGVCFs, please help~~ Thanks a lot! my CMD: java -Xmx60g -jar GenomeAnalysisTK-nightly-2016-09-23-gfade77f/GenomeAnalysisTK.jar -T...
View ArticleWhere might I download an hapmap for experimenting with GATK
Error messages beaucoup attend the use of VariantsToVCF tool in the following command line: java -jar gatk.jar -T VariantsToVCF -R reference.fa -o output1.vcf --variant:RawHapMap input.hapmap Having...
View ArticleCombining BAM files from two separate tests on same person, from same company
Hello. I poked around a bit but didn't find the answer. It was recommended to me that picard was appropriate for the task I have, but I was hoping for confirmation, and perhaps comments. My question...
View ArticleWhere can I get a gene list in RefSeq format?
1. About the RefSeq Format From the NCBI RefSeq website The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including...
View ArticleWhy are dbSNP indels excluded from indel realignment?
According to the known variants documentation (https://software.broadinstitute.org/gatk/guide/article?id=1247), only Mills indels and 1KG indels are recommended for indel realignment...
View ArticleWhat do numbers returned by BaseCountsBySample refer to?
I was expecting BaseCountsBySample to give the number of A, C, G and T bases at the position given by the POS column, but it seems like this is not the case. I have run HaplotypeCaller (version...
View ArticleVariantRecalibrator malformed header error
Hi can anyone please help me out with this error message from VariantRecalibrator: MESSAGE: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for...
View Articledata source questions
Hi I am Jiaming Liu, research associate from Genetrack Biolabs, Canada. Our company is planning to setup Next Generation Sequencing system for genetic diseases and cancer gene testing. My job is to...
View ArticleParsing CRAM files in htsjdk without a reference
I'm trying to convert some older code I have which used the older sam.jar system to read SAM/BAM files. One of the main reasons to migrate to htsjdk is to be able to read CRAM files. I've migrated the...
View ArticleMuTect2 Best Practice
I saw the new MuTect2 best practice here, with removing of indelrealignment. Does it apply to GATK 3.5/3.6 or the proposed GATK 4? https://software.broadinstitute.org/gatk/best-practices/mutect2.php
View ArticleBam not accepted by HaplotypeCaller
Hi there, Simulated some reads. My bam has around 400 reads.. trying to run haplotypecaller but getting error. Need help $ java -jar $GATK -T HaplotypeCaller -R ucsc.hg19.fasta -I pex_defaults_RG.bam...
View ArticleMutect HC+PON mode
Where could I find the vcf of normal panel to run Mutect in HC+PON mode? Thanks in advance. Giovanni
View ArticleGenotypeGVCFs --includeNonVariantSites emits reference as symbolic
Hi, It seems like starting with GATK 3.6 (or at least sometime after GATK 3.5), when running GenotypeGVCFs and emitting all bases with --includeNonVariantSites. Non-variant sites are now being emitted...
View Articleinstall picard-2.6.0
Hi, I have a trouble with installing picard-2.6.0. When I execute the command ./gradlew, the result shows the below. FAILURE: Build failed with an exception. Where: Build file...
View Article