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View Article*bam files with the same size (# of contigs) to merge?
Hi, I am trying to merge multiple (4 files data fom UCEs) *bam files using MergeSamFiles.jar. However, the script shows this message: Exception in thread "main"...
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View ArticleRead Groups without known barcodes
Dear all, I am working with some barley accessions but the barcodes for the samples are not known (not publicly available). However, because the addition of the read groups is a prerequisite for BQSR...
View ArticlePicard - SortSam
Hello, I'm using Picard's SortSam tool and was wandering if I can use the same script for 2 files? Meaning, can I do something like that (script below)? What would be the separator sign? Or I would...
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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...
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How to produce GVCF files that were produced from a different reference genome?
Hi everyone. I have got my genotyped vcf file successful produced but I needed to merge them with other g.vcf files I recently received from a collaborating company. These were gzipped vcf files with...
View ArticleWhy is gatk4 GetPileupSummaries always failed ?
I used the following command /home/projects/cu_10098/apps/src/gatk-4.beta.5/gatk-launch --javaOptions "-Xmx20g" GetPileupSummaries \ -R /home/databases/gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta...
View ArticleGATK4 resource bundle
Hi, I was wondering if you guys are planning to release a new resource bundle with full hg38 support (+patches)? Perhaps to celebrate the release of GATK4? Thanks M
View ArticleFiltering MuTect2 output for depth of coverage
Dear GATK team, I am writing with a question about depth of coverage in the output of MuTect2 (GATK3 and GATK4). I would like to filter my somatic calls to keep only calls with sufficient depth of...
View ArticlePL
Hi, I realize PL will be normalized in this page. https://www.broadinstitute.org/gatk/guide/tagged?tag=pl However, I need the data before normalize, raw PL, where can I get it? Thanks for your help....
View ArticleUsing GATK as part of a pipeline (licensing?)
I have a pipeline for analysing sequencing data, and one of the steps is a variant calling step using GATK. I'm thinking about somehow making my pipeline easy to run and then make it publicly available...
View ArticleSpam issues on the forum
You may have noticed that we're currently experiencing a surge in spamming on the forum. We're working with our host, Vanilla, to tighten our spam blockers and flood control measures. As part of that...
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