Problem in running Picard RevertSam
Dear Picard/GATK teams, I am using Picard v2.2.4 RevertSam tool. My command-line was: java -Djava.io.tmpdir=$TMP -Xmx30g -jar picard.jar RevertSam \ I=LP6005441-DNA_B07.modRG.bam \...
View ArticleMarkDuplicates Specific processes
java code MarkDuplicates and MarkDuplicatesWithMateCigar Function, Program specific algorithm process, can you say in detail, if can write the program directly according to the process.
View ArticleWhere can I get the GATK source code?
We distinguish "Classic GATK" (major versions 1 through 3) and GATK 4, the next generation of GATK tools. "Classic GATK" (major versions 1 through 3) (current distribution) We provide the current GATK...
View ArticleIdentify family relationships
Hi there, I've received a set of g.VCF files belonging to individuals of several different families and I've been asked to identify which samples belong together (same family) and what is the...
View ArticleSNP calling from RNAseq data
Hi, Do I need to do Indel Realignment and Base Recalibration while calling SNP from RNAseq data? If yes, then please share the command line. What are the parameter that should be used for raw VCF...
View ArticlePosters on somatic analysis with GATK4 presented at AACR 2017
A few of us GATKers (among a flood of other Broadies) traveled to Washington, DC this week for the General Meeting of the American Association for Cancer Research (AACR). Here are PDF copies of the...
View ArticleIs there Java version compatibility table, and can I download old versions of...
Thank you all for great software and active community. I'm trying to install and use but I faced a problem which someone already faced: Unsupported major.minor version 52.0 - do I need java 8? (howto)...
View ArticleDescription and examples of the steps in the CNV case and CNV PoN creation...
The CNV case and PoN workflows (description and examples) for earlier releases of GATK4. For a newer tutorial using GATK4's v1.0.0.0-alpha1.2.3 release (Version:0288cff-SNAPSHOT from September 2016),...
View ArticleChanging name of g.vcf files after combineGVCFs
Dear Sir/Madam, I'm running the combineGVCFs in order to create batches of 100 GVCFs. The job is running perfectly, reading first of all the 100 files with the proper name, but once is the combined...
View ArticleRead-Backed phasing and Indels
Hi, I'm calling Haplotypes of a diploid genome with the HaplotypeCaller and using the Read-Backed Phasing tool afterwards. I believe that Indels can't be phased so far. My output files look like the...
View ArticleIndel Realignment in Tumor-Normal pairs
Hello dear GATK team, I have a question regarding indel realignment when doing somatic variant calling (tumor normal pairs). First of all, I am aware that indel realignment is not required by mutect2...
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Which datasets should I use for reviewing or benchmarking purposes?
New WGS and WEx CEU trio BAM files We have sequenced at the Broad Institute and released to the 1000 Genomes Project the following datasets for the three members of the CEU trio (NA12878, NA12891 and...
View ArticleGATK supporting reads versus IGV display
Dear Staff Member(s), I hope you can help me clarify a discrepancy between GATK & IGV. The number of supporting reads that I see reported under sampleB.AltSupportingReads(AD) for a deletion is 5....
View Articlereadbackedphasing (HaplotypeCaller) outputs much more 0|1 then 1|0, why?
Hi! With the aim of phasing haplotype from SNPs of a single individual, I have used HaplotypeCaller which performes ReadBackedPhasing automatically (accuracy of SNP calling is beyond the question)....
View ArticleIs it necessary to cancel realignment for germline snp and indel calling in...
Hi , I find that the realignment step of Best Practice has been canceled! I do not know why ？ the following link is the Best Practice page I read....
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 Articleit's not accurate to use only one HaplotypeCaller gVCF as the input of...
HI , it's not accurate to use only one HaplotypeCaller gVCF as the input of GenotypeGVCF ？ if yes , how to prepare more gVCFs for my sample ? I just care the only one sample gVCF .
View Articlecan Mutect be used to detect somatic variants in healthy individuals?
Hi， We want to study the somatic variants in healthy individual with blood sample(cfDNA), can Mutect be used to detect this kind of variants? Thanks!
View ArticleHow to run MuTect v1 in Queue?
Hello, I'm trying to set up a queue script that runs MuTect v1 in parallel in scatter/gather mode combined with SGE. I'm using Queue-3.7 and my test script runs in dry-run mode, however when launching...
View ArticleErrors about input files having missing or incompatible contigs
These errors occur when the names or sizes of contigs don't match between input files. This is a classic problem that typically happens when you get some files from collaborators, you try to use them...
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