RealignerTargetCreator and IndelRealigner
Hi, The tools RealignerTargetCreator and IndelRealigner are obsolete in GATK4. Are there any replacements for these tools in GATK4? Also, there are two option -BQSR (used with PrintReads) and...
View ArticleReadBacked phasing vs Trio phasing?
I think I understand the technical difference. But in terms of phasing quality, how does one compare to the another? Are there any publications/reports/blog posts comparing the two? Is there some...
View ArticleHow does the BwaSpark in GATK4 control the number of threads?
I tried to ERR000589 process data with BwaSpark. The bam file size is 1.3G. The average time spent is about 25 min (5 nodes). However it would only cost 5 min in processing same data if I tried to use...
View ArticleGatherBamFiles / FixMateInformation / ValidateSamFile
Hi, here the pipe... 1) ApplyBQSR while read -r f1 f2; do .... ${ph6} --java-options ${java_opt1} ApplyBQSR -R ${gnm} -I ${fBAM} -O ${fol5}/${c_applybqsr} -L ${f1} -bqsr ${fol5}/${bqsrrd}...
View ArticleBiallelic vs Multiallelic sites
A biallelic site is a specific locus in a genome that contains two observed alleles, counting the reference as one, and therefore allowing for one variant allele. In practical terms, this is what you...
View ArticleGATK 4.0 does not have the IndelRealigner method?
HI，I found that the LATEST version of GATK 4.0 does not have the RealignerTargetCreator and IndelRealigner modules！ Is that means we don't need them any more?
View ArticleProblem with annotating GATK4 VCF file
Hi Based on GATK4 best practices pipline I have made a VCF file composed 4 person WES data. When I want to annotate it with annovar , but annovar could not annotate all variations and near 70% of...
View ArticleConfusion in using gVCF mode
Hi I have problem in using HaplotypeCaller gVCF mode ( GATK4 best practices). Please let me know following problems: 1- Should we run gVCF even when we have one WES sample? 2- I have 3 WES samples,...
View Articleextracting forward and reverse reads from uBAM file
Hi everyone, I am using Ion 16s Metagenomics kit to perform microbiome analysis in wastewater. After performing paired-end sequencing, I have been given raw reads in a UBAM file which contains both...
View Article[GATK 4.0.1.2] No non-zero singular values were found in creating a panel of...
Hello, I got an exception below in creating a PoN for somatic CNV on about 80 WGS samples. It consists of ~30 males and ~50 females. I was able to create PoNs successfully for each sex separately, but...
View ArticleA GATK RUNTIME ERROR, Invalid alignment found, alignmentStart > alignemntEnd
Hi, I was in the second step of Genome STRiP, to discover SV. It seems that all "partition" jobs worked fine, except one. The error message looks like this: ERROR 00:12:01,906 FunctionEdge - Contents...
View ArticleMutect2 outputting samples with AD of "."
I've setup a workflow that runs Mutect2, which completes successfully, but the AD of all variants is output as "." This is an issue as we use the AD for downstream stages. Is there any reason this...
View ArticleCombineVariants Key . found in VariantContext field INFO but this key isn't...
I have encountered the following error when trying to merge two VCFs from different callers: Key . found in VariantContext field INFO at chrM:711 but this key isn't defined in the VCFHeader. We require...
View ArticleGermline VQSR recommended settings
Hi, we've been looking at the new Best Practices pages and at the WDLs linked there. In particular, we looked at the settings for VariantRecalibrator in this WDL. We ran germline analyses on samples...
View Articlegatk3.8 vs gatk4 va gatk4spark ,the newer the slower!!
I use the gatk3.8 gatk4.0.0and gatkspark to test my data . I received a suprising result. gatk4 is slower than gatk3.8 ,and gatkspark is slower than them. The times are 17.3 vs 19.2 vs 24 min . The...
View ArticleGenotypeGVCFs error
Hi I am getting the following error. I ran the exact same samples/pipeline a couple of weeks ago using 3.6 and it worked fine, now with 3.7 I am getting an error: INFO 09:49:49,742 HelpFormatter -...
View ArticleOpenMP multi-threaded AVX-accelerated native PairHMM in HaplotypeCaller not...
I'm unable to get a multithreaded instance of PairHMM to work in HaplotypeCaller with JDK 1.8 on my local machine (Intel 4770K 8-core i7 processor) running MacOS 10.12.6. I've tried both a pre-built...
View ArticleRegarding of piping - Picard and BWA (Align and MergeBamAlignment step)
I made 3 bam files with **command in below.** Picard version: 2.17.8 BWA version: 0.7.17-r1188 compression_level=2 java_opt="-Xmx32G" bwa_version="0.7.17-r1188" bwa_commandline="mem -K 100000000 -p -v...
View ArticleCurrent status of GATK4 GermlineCNVCaller tools and best practices.
Hi, I would like to try out GATK4 for discovering or genotyping germline CNV's in a cohort of few hundred whole genome sequenced samples. I work with non-human species data, but the genome sizes are...
View ArticleGATK - 4.0.0.0 [BaseRecalibratorSpark low performance]
Dear GATK_team, I'd like to run Spark-enabled GATK tools on a Spark cluster. Precisely I am launching a Spark cluster in the standalone mode submitting the BaseRecalibratorSpark application via Slurm....
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