ArrayIndexOutOfBoundsException error in BaseRecalibratorSpark
Hi, Thank you for your time. I ran BaseRecalibratorSpark with GATK4 and GATK4-protected on Amazon instance. Both of them gave me error java.lang.ArrayIndexOutOfBoundsException: 1073741865. When running...
View ArticleGATK VariantRecalibrator failed on Bad input: Values for MQ annotation not...
I run the HaplotypeCaller first and the output is gvcf. I check the input gcvf file, there is no MQ value instead of RAW_MQ. Any idea about this issue. My data sets is 40 whole genome sequences. Thanks
View ArticleReplace UnifiedGenotyper with HaplotypeCaller
I have been trying to genotype a list of given positions from BAMs files. Until today I used UnifiedGenotyper This was my command and it works fantastic: FOR %%i IN (*.bam) DO java -jar...
View ArticleMethods for subsetting gvcf
Greetings, Is there a proper way to subset a gvcf file created from HaplotypeCaller? I have a large number of gvcf files from various sequence projects, including whole exome. I was trying to subset...
View ArticleDeduping AFTER BQSR
Is there any justification for putting off the MarkDuplicates step until after you've run BQSR? Based on my knowledge of bioinformatics, this seems like a dangerous idea, but it's the one recommended...
View Articlegetting HaplotypeCaller to work
Hi all, I am new to WGS analysis. I have paired end reads, so I used 'bwa mem' to get the .sam file and then samtools to create the .bam. Next the sorting and marking duplicates has been done with...
View ArticleSame mutation from different samples are differently annotated in dbsnp database
Hello, I try to call mutations for several samples by using mutect2. For some samples (such as WES443), a mutation of interest (chr2:201113112 based on hg19) is successfully annotated in dbSNP database...
View ArticleA 50 bp insertion (INDEL) varaint calling
Hi All, I am using both UnifiedGenotyper and HaplotypeCaller to genotype given alleles from amplicon based sequencing data. It seems that both caller did not performe well on variant rs1799752, a 50 bp...
View ArticleDownsampling
Downsampling is a process by which read depth is reduced, either at a particular position or within a region. Normal sequencing and alignment protocols can often yield pileups with vast numbers of...
View ArticleUpcoming GATK events in July : UK workshops and BOSC 17
We've been getting so caught up in the excitement of the imminent beta release of GATK4 (possibly later this week!), we forgot to announce upcoming workshops! And two of them are coming up fast, in...
View ArticleHaplotype Caller caller error in GATKv3.6
Hi, Sample is NA12878 and HC runs on this sample routinely as part of our testing. This runtime error seems to be sporadic. ERROR MESSAGE from HC is below INFO 14:08:15,398 ProgressMeter - 16:28875483...
View Article(howto) Install all software packages required to follow the GATK Best...
Objective Install all software packages required to follow the GATK Best Practices. Prerequisites To follow these instructions, you will need to have a basic understanding of the meaning of the...
View ArticlePICARD MarkDuplicates errors near the end of its process: tmp does not exist
Hi, I have a problem in that PICARD MarkDuplicates appears to error near the end of its process -- with a temp file not found error. This is running in a GATK pipeline on our cluster for WGS Best...
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 ArticleSetting Up a Cromwell VM
Hi, My group is interested in setting up a dedicated Cromwell VM and would like advice on storage, cpu, and memory recommendations for this. We'll be running a number of different pipelines on this VM...
View ArticleHaplotypeCaller not calling variants overlapping with active region and...
We've been running regression tests of HaplotypeCaller against previous UnifiedGenotyper output and we found a locus where UG originally called a set of 4 low allele balance SNPs while HC produced no...
View ArticleHow do I fix the error Provider...
The command I'm running: spark-submit --master yarn --conf spark.driver.maxResultSize=0 --conf spark.driver.userClassPathFirst=true --conf spark.executor.userClassPathFirst=true --conf...
View ArticleHaplotypeCaller - ploidy for pooled samples of bacterial genomes
Hello, I have an experiment where I've sequenced pools of individuals from bacterial populations. Based on the guidelines for setting ploidy, I think I should set this to the average read depth because...
View ArticleRequest to only warn when a base quality greater than 60 is encountered.
Unfortunately some GATK tools do not accept a base quality greater than 60. Instead of warning the user, or capping the quality, the tool exits with an exception. The relevant maximum is defined here:...
View ArticleNot masked low quality sites using FastaAlternateReferenceMaker
Dear GATK Team.., I intend to mask variants that have low quality (DP less than 8) using Fasta Alternate Reference Maker. First, I select variant using SelectVariant with command below: Low quality...
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