Abnormally high per-sample depth after running GenotypeGVCFs
I first posted this question as a reply to something related (see https://gatkforums.broadinstitute.org/gatk/discussion/7318/what-is-the-significance-of-depth-across-all-samples-dp-in-info#latest) but...
View ArticleStrange RevertSam error
I recently came across this error using RevertSam, and haven't been able to find forums related to this issue. Any idea what might be causing this? To get help, see...
View Articlefile size - Haplotypecaller input file - > correlation with output *.g.vcf file
I have been making several g.vcf-files by Haplotpecaller, for later combined variantcalling. Usually there has been a reasonable correlation between the input recal*.bam file and the output g.vcf file....
View ArticleWhere to find CreateSequenceDictionary.jar?
I've downloaded the recent GATK 3.7-0 release, which does not include CreateSequenceDictionary.jar. Is the following command replaced by something new? java -jar CreateSequenceDictionary.jar R=...
View ArticleHow to get nonvariant sites without the ref N sites.
I'm trying to get a vcf with the invariant sites i.e. select out ONLY the homozygous references sites in a multi-sample vcf (samples are either all 0/0 or a mix of 0/0 and ./.). I do not want the sites...
View Articleto get the same results, must add -pairHMM LOGLESS_CACHING when I use the...
Dear Dr. Geraldine I have read https://gatkforums.broadinstitute.org/gatk/discussion/comment/40473#Comment_40473 about the reproduce questions. And I want to ask weather I must add -pairHMM...
View ArticleHow to use bwa mem for paired-end Illumina reads
Dear All, we would like to use the bwa mem algorithm for the alignment of paired-end (100 bp) Illumina reads and variant calling with GATK. Unfortunately there are some problems understanding the...
View ArticleDocumentation disappeared
It used to be that when you went to upload a data file there would be a link to documentation (see attached screenshot). The user guide link used to take you to documentation about how to upload data...
View ArticleClik here to view.
picard liftovervcf parsing error
I am using picard liftover vcf to algin variants from hg38 to hg19. I am not sure what the error is referring to though it seems to be an issue with the vcf (I have copied a few lines of the format)....
View ArticleLiftoverVariants error, chain file you are using is not compatible
I'm trying to liftover the GATK bundle hg19 .vcf files to GRCh38 and encountering an error with LiftoverVariants from GATK 3.3.0. java -Xmx12g -jar $gatkpath \ # GATK 3.3.0 -T LiftoverVariants \ -R...
View ArticleClik here to view.
How long does it take, Part 2
A while back, I posted this article about work done by the Intel Bio Team to benchmark the speed and resource utilization of each step in the per-sample segment of the germline variation pipeline...
View ArticleAre there sample WDL workflows for GATK4?
I looked in github.com/broadinstitute/wdl and there was only one script, PreProcessingForVariantDiscovery_GATK4.wdl It would be useful to have other sample workflows for germline/somatic calling, CNV,...
View ArticleWhen I use the FastqToSam to convert my fastqfiles to bam, there are 4 lanes
When I use the FastqToSam to convert my fastqfiles to bam, there are 4 lanes each have two fast files(read1, read2) which lane should I choose?
View ArticleGetBayesianHetCoverage exits with code 247
When I run GetBayesianHetCoverage in a Docker container, the function exits without completing with code 247. The Docker container is built from an image that uses the Debian "Stretch" base image, with...
View ArticleCan I use merge step after getting gvcf files for RNA-seq data
https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS&p=2 On this page, mentioned by the first sentence that "this step only applies to DNA workflow". Can I use...
View ArticleMUTECT helo interpreted it
Dear, I have executed the mutect and I am not understand the result. In the example below. The variants are present in COSMIC, but were REJECT by the MUTECT filter. Could you explain the reason??...
View ArticleClik here to view.
HS_LIBRARY_SIZE = "" (that's right, nothing, empty) HS_PENALTY_XX are all 0
So I've ran both the newest version of Picard CollectHsMetrics and an older version CalculateHsMetrics and with both versions I'm getting statistics for everything but the HS_LIBRARY_SIZE which has an...
View ArticleClik here to view.
What is the difference in allele frequency reported as "0" (zero) and "." ?
What is the difference in allele frequency reported as "0" (zero) and "." ?
View ArticleDangling heads and tails
Hello, The logic for merging dangling tails appears to be different from that for dangling heads. For example, it looks like tails can be merged to a non-reference path while heads cannot. Is there a...
View ArticleAllelic CNV (common snps and getbayesianhetcoverage
I created a list of common SNPs for GetBayesianHetCoverage following https://gatkforums.broadinstitute.org/gatk/discussion/7812/creating-a-list-of-common-snps-for-use-with-getbayesianhetcoverage. I...
View Article