Errors about input files having missing or incompatible contigs
These errors occur when the names or sizes of contigs don't match between input files. This is a classic problem that typically happens when you get some files from collaborators, you try to use them...
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View ArticleQuestion about MutSig1.4
I am trying to run MutSig for indels using the script below...
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View ArticleCOSMIC and dbSNP files for MuTect
I'm having trouble finding the recommended COSMIC and dbSNP file for hg19 to use with MuTect (hg19_cosmic_v54_120711.vcf and dbsnp_132_b37.leftAligned.vcf). I can't find these in any of the bundles on...
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 Articlebcbio configuration file (bcbio_system.yaml)
Hello! I have a question regarding how to tune options for specific software (gatk) in bcbio conf file (bcbio_system.yaml). I want to define GATK PrintReads java memory parameters Xmx like this:...
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View ArticleUnifiedGenotyper error: Somehow the requested coordinate is not covered by...
Dear GATK Team, I am receiving the following error while running GATK 1.6. Unfortunately, for project consistency I cannot update to a more recent version of GATK and would at least wish to understand...
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Dear GATK team, Could you please delete my account? Thank you in advance and best regards, Tiziano
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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 ArticleIMPORTANT -- Bug alert for GATK4 GenomicsDBImport
We have identified a major bug in the GenomicsDBImport tool that affects all released beta versions of GATK4 up to 4.beta.5 (inclusive). The bug occurs under specific conditions (detailed below) and...
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