Picard AddOrReplaceReadGroups Error: Read CIGAR M operator maps off end of...
Hello! I have bam files generated by Illumina's CASAVA pipeline, and the reference genome version in the accompanying document is 'NCBI37_UCSC'. when I use GATK RealignerTargetCreator to do Local...
View ArticleI ran the CollectAlignmentSummaryMetrics on a bam file and got this error...
java -jar picard.jar CollectAlignmentSummaryMetrics R=Homo_sapiens_sequence_hg19.fa I=KAPALibPrep_cfDNA_B08_S14_sorted.bam.bam O= KAPA-cfDNA_B08_metrics To get help, see...
View ArticleSplitNCigarReads uses more than 1 core with no options to set number of cores...
If running on a cluster system that kills jobs if they use more than their allocation, you need to be able to either know how many cores are required or be able to limit the number of cores used. Are...
View ArticleGATK4_acnv problems
Hi We ran into some GATK4_acnv failures while processing StandUp2Cancer exomes this weekend using gs://fc-099b74a5-b2e1-4f8c-8720-2ab7123fe631/ref_data/gatk-package-4.beta.1-local.jar We've run this...
View ArticleI am running Picard ValidateSamFile on my Bam file and got this error below....
java -jar picard.jar ValidateSamFile I=KAPALibPrep_cfDNA_B08_S14_sorted.bam.bam MODE= SUMMARY HISTOGRAM java.lang.String Error Type Count ERROR:INVALID_CIGAR 40 WARNING:MISSING_TAG_NM 35183540 I am...
View ArticleHaplotypeCaller warnings DepthPerSampleHC
Hi I'm trying to do a multisample variant call using several bam files in the following cmd /mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk HaplotypeCaller -R /mnt/fastdata/md1jale/reference/hs37d5.fa...
View ArticleWhy is it so slow to download the GATK resource bundle through Broad ftp?
I tried to download from ftp://ftp.broadinstitute.org/bundle/b37/ but it is very slow. Is it normal?
View ArticleLiftoverVcf no output
Hi! I'm using LiftoverVcf to make a hg38 version of the gnomad file from the GATK resource bundle The gnomad file is in b37 version, as there isn't a chain file for b37 -> hg38, I have to do b37...
View ArticleNullPointerException in HaplotypeCaller 4.0.1.1
Dear GATK team I am calling variants using HaplotypeCaller on both WGS data form a normal tissue samle and RNA seq data on tumor tissue. Settings for HC are slightly different for the RNA seq data but...
View ArticleWhy does Mutect2 @ GATK4 breaks everytime when running on single tumor mode?
Hi, I have been using Mutect2 in tumor-normal mode, to create PON and now I am trying Mutect2 single tumor mode. The program fails every time with sometimes 10 and sometimes 15 chromosomes, and is...
View ArticleAny extra filters when using Haloplex or amplicon sequencing data?
Hello everyone! Our group has a Haloplex dataset from the old days when Agilent wasn't marking the PCR duplicates with barcodes. So unfortunately, deduplication is out of question. 61 genes were...
View ArticleIndelRealigner replacement
Hi, I have been using GATK IndelRealigner in non-GATK pipelines, and was wondering if there was a replacement option in the current GATK version, or if I should keep using the old version of GATK for...
View ArticleReadBackedPhasing MNP phasing call
Can the tool also work on MNP other than SNP? If not, is there any plan to expand?
View ArticleHow to edit MULTIPLE read groups in one bam file
Hi everyone, I recently received a WGS bam from Broad for 1 sample, but with about 8 read groups. BSQR kicked it back saying that the sequencer name in the read group is not recognized. Anyways, I need...
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Not calling all sites in gvcf option (bp_resolution)
Dear GATK team, I am trying to call all possible sites in my targeted interval (BED) with GATK HaplotypeCaller -ERC BP_RESOLUTION. But I have for example: chr 9 134842581 . A chr 9 134842583 . C GATK...
View ArticleBCL to uBAM tutorial update
Hi there, I'm very interested on try the BCL to uBAM protocol (Tutorial#6570 coming soon) you have mentioned on your article #6483 ((How to) Map and clean up short read sequence data efficiently). Do...
View ArticleCan GATK accepts more than one bed file while computing depth of coverage?
Group1.BAMfiles.list has three BAM files: Sample_001/SAM001.clean.dedup.recal.bam Sample_002/SAM002.clean.dedup.recal.bam Sample_003/SAM003.clean.dedup.recal.bam Group1.BED has three BED files:...
View Article(howto) Apply hard filters to a call set
Objective Apply hard filters to a variant callset that is too small for VQSR or for which truth/training sets are not available. Caveat This document is intended to illustrate how to compose and run...
View ArticleMost efficient way to combine multiple GVCF files
Dear GATK team, In order to calculate variant frequencies, all samples from different runs must be in the same GVCF. For each run, I'am currently running the CombineGVCF tool and then I use the...
View ArticlePicard in Docker
Dear GATK/Picard team, I am new to Picard and was just about to build it, when I noticed that there is a Picard Docker image available - great idea! Is this functional yet? I couldn't find any...
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