Cannot connect to the ftp server
Hello, I tried to connect ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/ , but I got a "530 Login incorrect". Would you please check that? Thanks for your help, Henry
View Article(howto) Test your Queue installation
Objective Test that Queue is correctly installed, and that the supporting tools like Java are in your path. Prerequisites Basic familiarity with the command-line environment Understand what is a PATH...
View ArticleAddOrReplaceReadGroups
I am processing single-cell RNAseq data which I downloaded using GEO accession number (it was in .sra format which I converted to .bam) Now I'm trying to run the scRNAseq pipeline and got stuck since...
View ArticleAccess bundle
Dear gatk team, I am struggle with an issue, it's 4 day that I try to access the resource bundle without success. I am following the steps posted in the page, as username: gsapubftp-anonymous and as...
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9 Takeaways to help you get started with GRCh38
We are starting official support of GRCh38, a reference genome with alternate contigs. In fact, going forward all of our new projects will use GRCh38. During this transition over the coming year, we...
View ArticleGATK 3.8 log4j error
I just upgraded from GATK 3.7 to the newly released GATK 3.8 (3.8-0-ge9d806836) and I am getting a StatusLogger error: ERROR StatusLogger Unable to create class...
View ArticleMNP calling problem in GATK4 Mutect2 beta
Hi, I tried to use GATK4 Mutect2 to call somatic mutations and found some weird MNP results: CHROM POS REF ALT chr2 157214886 GT TT chr4 130772884 CGTGT TGTGT chr4 145617203 TAAA AAAA chr5 7857891 CAA...
View ArticleMutect2: INFO field PON never reported
Hi- I'm using Mutect2 from GenomeAnalysisTK-3.8-0-ge9d806836, everything looks good but I noticed that the vcf header of the output contains the INFO:...
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Should I analyze my samples alone or together?
Together is (almost always) better than alone We recommend performing variant discovery in a way that enables joint analysis of multiple samples, as laid out in our Best Practices workflow. That...
View Articlepicard CalculateHsMetrics/CollectHsMetrics got stuck somewhere
I ran the following command java -Xmx130g -Xms80g -Djava.io.tmpdir=javatmp/ -jar ~/picard.jar CollectHsMetrics BAIT_INTERVALS=annotations/NexteraRapidCapture_Exome_Probes_v1.2.interval_list...
View Articlejava.lang.NumberFormatException: For input string: "R"
I am attempting to run Churchill, a pipeline that is designed to speed up variant calling on whole genomes and run into the error I post below. I've read several threads on this site that discuss the...
View ArticleVariantFiltration: vcf and reference have incompatible contigs
Hi, I got an error during VariantFiltration step stating " GATK_All_Variants.vcf and reference have incompatible contigs. Please see...
View ArticleMutect2 parallel problem
Dear GATK team. I am using Mutect2 to call somatic mutation from tumor/normal paired sample. However after jobs running for 8 days, our server has been rebooted for some reason. Most of the jobs are...
View ArticleDoes GATK4 open the FPGA port in BWA for accelerating?
We are working on the FPGA accelerating in BWA, does GATK4 open the relative port? THX.
View ArticleWhy is HaplotypeCaller calling very few variants
Hello, I am currently working on a benchmark analysis using different variant calling methods, including your HaplotypeCaller algorithm, using version 3.7. However the results I am getting from your...
View ArticleRegarding GenderMap file in genomestrip
Hello, Can someone tell me that what should i define gender for plant sample in gendermap file. Please explain me?? Thank you in Advance
View ArticleAre RGQ values greater than 99 valid?
I have two questions with regard to RGQ and the --includeNonVariantSites flag in GenotypeGVCFs: 1) I have read in another thread that GQ and RGQ are capped at 99. However, I am seeing values that go...
View ArticleRealignerTargetCreator hangs
Hi GATK team! we have an issue with running the RealignerTargetCreator unfortunately. Commandline looks like this: gatk -T RealignerTargetCreator -R ref.fasta -I /testsample.sorted.bam -nt 32 -o...
View ArticleThe result of Mutect BAM and vcf is different.
I got some vcf result using mutect. but I have some question about the result. the Allele frequency in vcf is so strange. for example, the below is my result. chr4 1809127 . C T ....
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