Can ASEReadCounter take indels?
Can ASEReadCounter calculate allele-specific count correctly on indels? I've seen some old posts about a bug for this (https://gatkforums.broadinstitute.org/gatk/discussion/6723). I wonder if it was...
View Article[PICARD] CollectInsertSizeMetrics vs CollectAlignmentSummaryMetrics
Hello, I am getting some confusing results and not sure how to explain them. I am interested in the total number of reads from a PE library that actually mapped to our reference so we can take that...
View ArticleWhere to download Normal exome bam for creating PoN for cancer CNV workflow
Hi, We are trying to get the copy number variation of the tumor only samples (from bam files) using the below workflow (not having paired normal samples)...
View Articlejava.io.IOException: Read end dead
I met the problem using picard. so I checked the bam file. It had no error. java -Xmx12G -jar /BiO/Install/picard-2.17.10/picard.jar GatherBamFiles...
View ArticlePerformance troubleshooting tips for GenotypeGVCFs
Hi, I am running a GATK4 variant calling analysis on few hundred Solanum lycopersicum samples via bcbio (species is diploid, 1gigaBase reference) . Everything went fine up to and including importing to...
View ArticleHow can I access the documents/articles found in a post?
When I tried to click on an article/document linked in the "HaplotypeCaller in a nutshell" post, it gave me the following message: Error retrieving content: Could not load requested content from the...
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Error in GatherBQSRReports
Hi, starting from WES pair-end data... in the BaseRecalibrator step I used as interval these regions/chr: chr1-22, chrX, chrY, chrM, alternative contings and HLA contings. In the case of HLAname I...
View ArticleHow to command RPA Bot to Iterate name in dropdown using workfusion.
I am utilizing workfusion to mechanize the manual procedure yet in the initial step the client need to choose worker name from the dropdown or the client can type the name to channel. It works on the...
View ArticleAny ploidy goes!
Until now, HaplotypeCaller was only capable of calling variants in diploid organisms due to some assumptions made in the underlying algorithms. I'm happy to announce that we now have a generalized...
View Articleoverlapping read pairs in GATK 4.0.1.2
Hi, I came across this post regarding overlapping read pair: https://gatkforums.broadinstitute.org/gatk/discussion/1745/does-unifiedgenotyper-count-overlapping-paired-end-reads-as-two-separate-reads I...
View Articlerunning haplotypeCaller using Queue
I wrote my first script in scala to run haplotyperCaller walker of GATK. However, I am running into some errors when I execute the *.scala script. I am unable to figure out the source of error, any...
View ArticleMutect2 Oncotator failed to delocalize files
I tried to run Mutect2 with Oncotator in FireCloud and it seems like Cromwell is having trouble copying files, though I don't know what that means. I got the following error message. Task...
View ArticleCNVdiscovery pipeline: Argument with name '--genderMapFile /'--ploidyMapFile'...
I'm testing the CNVdiscovery pipeline on a small set of individuals and I can't seem to get it running. I keep getting the following error despite both the gender & ploidy map being an optional...
View ArticlePicard or GATK tools
Hi, some picard tools like MergeSamFiles were ported to GATK 4 beta. Now in the release version they are described as picard tools again. Even though they are part of the GATK and can be used as such....
View ArticleUnable to run SVPreprocess. Java cannot find the main class
Hello. I'm sure this is obvious but I can't seem to find my bug. I have been trying to execute the commands as listed in the documentation for our data but I am thwarted at every turn. Here are the...
View ArticleGenomicsDBImport too slow on local server
Hi, I tried using GenomicsDBImport for our data. In my testcase I tried importing Chromosome 1 for 223 samples. Since most samples are panels and we have only a few genomes and exomes, I thought it...
View Article[GATK 4.0.1.2] unsorted bam in mutect pipeline running in tumor-only mode...
Hello, I need your help on using Mutect2. I tried to call somatic mutations using mutect2_multi_sample.wdl in tumor-only mode with make_bamout = true and scatter_count = 50. It was failed for a small...
View Article[GATK 4.0.0.0] Allelic copy number
First, thank you very much for this great tool (GATK4). Copy number profil even with targeted sequecing are now much more accurate with or without a matched normal. But now i wonder if it's possible to...
View ArticlePicard: FixMateInformation crash
Hello, I was asked to re-post this question here. It was originally posted in the Picard forum at GitHub at https://github.com/broadinstitute/picard/issues/161. Regards, Bernt ORIGINAL POST (edited)...
View ArticleWGS+WES combined discovery/genotyping
Hi GATK team, Hope you had great holidays! We're analyzing small families where some individual have been sequenced by WES (HiSeqX) and others by WES (HiSeq4000). Could you please advise on the best...
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