How does GATK4 Accept Sharded Data and SNP&Indels calling Pipeline
We found that many GATK4 commands accept an option to let them output "sharded" files. But we didn't find how those commands accept "sharded" data that generated from the last step. For example, gatk...
View ArticleA USER ERROR has occurred: couldn't write file because writing failed with...
The command I'm running: spark-submit $JAR gatk-package-4.alpha.2-1147-g1477e1c-SNAPSHOT-local.jar PrintReadsSpark \ -I gs://mybucket/newbam.sort.bam \ -O gs://mybucket/outputfinalspark.bam The error:...
View ArticleGATK HaplotypeCaller does not forward @PG BAM header lines to -bamout
Hey GATK Devs! I'm using GATK (v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18) to call SNPs and Indels on a single sample. The reads were aligned with BWA (v0.7.12) and duplicates marked with Picard...
View ArticleDetails on how Picard-Tools define duplicate reads
Dear colleagues, I am trying to implement a script to group duplicate reads into families and would like to understand which criteria Picard's MarkDuplicates uses. I've read that it compares the 5'...
View ArticleGATK runtime error (READ_MAX_LENGTH must be > 0 but got 0) with 1000g bam
Hi, I'm trying to build a pon with GATK 3.7-0 to use with mutect2. For that, I've downloaded 80 exome bam files from the 1000g project (GBR, TSI, IBS and CEU populations). For most of them, when I try...
View ArticleHow to call somatic mutation if I have only tumor sample when exome sequencing
Hello, some tumor samples from FFPE are absent from normal control, we performed exome sequencing. In this situation, how to detect somatic mutation?
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What is a GVCF and how is it different from a 'regular' VCF?
Overview GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF (see the spec documentation here), but a Genomic VCF contains extra...
View ArticleWhat is happening regarding Picard tools and NovaSeq?
Hi, I got picard 2.9.4 in order to get the support for CBCL files, i.e. NovaSeq output. There was a command line option 'USE_NEW_CONVERTER' added to IlluminaBasecallsToSam. Now in 2.10.0 that...
View ArticleHaplotypeCaller crashes (GATK v3.7)
Hi everyone, i wondered if anybody else saw something like this happening. At first, I had issues with running a "normal" HaplotypeCaller command on a BAM file on our linux machine/server and thought...
View ArticleTrimming of Adaptor sequence?
I have heard we can import raw data into GATK pipeline without trimming the adaptors. Is it not necessary to remove adaptors from the sequence? Also, I have asked the same questions in different blog....
View ArticleDisconcordance between chip run for same sample
Hi all, I am evaluating the panel performance, which was designed based on amplicon enrichment. However, I found that 2 out of 2000 variants showed disconcordance between the two run. For example,...
View ArticleVariantsToVCF Error: Null alleles are not supported
Hi GATK team, I am trying to convert HapMap output files of TASSEL3 to VCF using the GATK VariantsToVCF tool. However, I am getting the error below. I used GATK v3.2-2-gec30cee. Do the "null genotypes"...
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Bug: HaplotypeCaller -drf
If I call HaplotypeCaller with --help it says that with -drf I can name "read filters to disable". Notice the plural. So I assume disabling multiple filters must be possible somehow. I'm trying to find...
View ArticleHaplotypeCaller: INFO report -> odd values
There are 68 reads covering my SNP of interest: samtools view mybam.bam 6:1611802-1611802 | wc -l 68 This matches what I see in IGV (after turning off all the filters in the preferences of course!)....
View ArticleMutect2 --artifact_detection_mode
hi, could anyone share how Mutect2 identifies artifacts? I suppose those are from sequencing/mapping errors. Thanks!
View Articleadditional header line throws an error (e.g. using @GA)
Hello, Within the HUPO PSI, we are devising novel proteogenomics data standards that are extension to the SAM/BAM format housing mass spectrometry information (see http://www.psidev.info/proBAM). I’m...
View Articlepositive and negative set in model training by variantRecalibrator
Hello! Thanks for develop this tool set and share with others with good supports, it really contains a lot of wonderful tools. I just try to understand VQSR more into detail. If I give the resources...
View Articlesome questions about difference between HaplotypeCaller and MuTect2
Hi, Recently I have been worked in variant calling using GATK and I have some questions in the process of learning GATK tools. I’m interested in the essential difference between HaplotyepCaller and...
View ArticleCalculateGenotypePosteriors error
Hi, I've run the GATK best practices pipeline up through VQSR and have the recalibrated variants in a VCF file. Because I'm analyzing pedigree samples, I'm now attempting to run...
View ArticleHow to force MuTect2 genotype all sites within intervals?
I cannot generate genotypes for all input sites with MuTect2 (-L input.vcf). I tried --output_mode EMIT_ALL_SITES and -gt_mode GENOTYPE_GIVEN_ALLELES without luck. Is there an equivalent option to...
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