there aren't enough columns for line 96340 when GenotypeGVCFs
ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version 3.6-0-g89b7209): ERROR ERROR This means that one or more...
View ArticleSomatic Mutation Identification without Matched Normal Sample -- WES
Is there any tools, workflow or pipeline to identify somatic mutations without matched normal sample? We have data only for WES of tumor samples.
View ArticleGATK (v 3.5) VariantAnnotator ERROR: potential bug?
Hi, I am using VariantAnnotator and, among other annotations, I would like to add also the allelic frequency of my SNPs in 1000G to the resulting annotated .vcf file. I did this through the following...
View ArticleGATK4 fails in BwaSpark most likely due to splitting
Running GATK4 BwaSpark encounter the following fatal error message: [M::mem_sam_pe] Paired reads have different names: "206B4ABXX100825:7:66:2632:21260", "206B4ABXX100825:7:66:2632:31752" Script:...
View ArticleRNA-seq and WGS for cancer samples (no paired T-N)
Dear GATK Team, I want to do SNP calling on cancer RNA-seq data (no matching normals). In some cases I have matching WGS data (for which I also want to do SNP calling) - but not for most cases. If I...
View ArticleSplitNCigarReads exception
my script : java -jar ~/bin/gatk-3.2-2/GenomeAnalysisTK.jar -T SplitNCigarReads -R Gmax.fa -I NPB18L_mark.bam -o NPB18L_snc.bam -U ALLOW_N_CIGAR_READS -fixNDN when i use -fixNDN, it will be:...
View ArticleGenotypeGVCFs output IUB code *
Hi. I found that in some case, GenotypeGVCFs may output IUB code * (such as G,* )into vcf. What is the meaning of "" and how to remove the "" from ALTs ? GATK Version 3.4.0-46 Command: java -jar...
View ArticleIndelRealigner Not attempting realignment in interval
Hi, first of all, sorry, if I'm not correct in this forum, but I didn't find a place where it realy seemed correct. On the last data I've got I ren into information like: "INFO 22:14:12,352...
View ArticleVariantsToTable question
Hi there, When using the VariantsToTable function, is there a way to force the genotypes to be numeric, i.e. 0/1 or 0/0 rather than the actual bases like G/T, G/G, etc.? I can't seem to find anything...
View ArticleVQSR training set
Hi all, I would like to try applying VQSR to my WGS data. What I could use is a SNP database built with GBS on different samples than the ones present in my actual callset. I have a question: do we...
View ArticleGenomeSTRiP Runtime Error: Cannot handle multiple junction records
I am getting the error message below when genotyping a list of deletions (generated by another sv program) with GenomeSTRiP.. Are there any workarounds/solutions for this? I am getting this error...
View ArticleWriting a custom...
I'm playing with the package org.broadinstitute.gatk.tools.walkers.annotator and I wonder if I can write the following custom variant annotator: I've got a set of tabix-ed files in a directory (one...
View ArticleCombineVariants - duplicate reads are generated for the same chr:pos
I am merging two VCFs. the records are as below VCF1: CHROM POS ID REF ALT QUAL 1 1247578 . TG TGG,TGGG,TGGGG,TGGGGG,T,TGGGGGG 53367.32 VCF2: CHROM POS ID REF ALT QUAL 1 1247578 . TG...
View ArticleHow to uncap GQ?
Hi, I know the GQ is capped to 99 in the current setting but I wonder if there is a way to uncap the GQ. Thank you!
View ArticleMuTect2 high insertion counts?
Hi Folks I am using Mutect2 to analyze blood vs. FFPE tumor samples (breast cancer). I am getting (what I think are) unusually high insertion:SNV ratios - the ratio is between 2:1 and 3:1, thus high...
View ArticleReadBackedPhasing Read Depths
Is it intended that ReadBackedPhasing does not propagate the read depths of merged SNVs (and if so, why not)? My lab is considering going back to the original and getting the minimum read depth and...
View ArticlePhasing via HaplotypeCaller vs. ReadBackedPhasing
I recently started running ReadBackedPhasing in the interest of correctly deducing which variants were MNPs, which got me to looking at the phasing information represented. I know in a GATK FAQ it is...
View Articlelocal realignment of tumor and normal pair samples
Hi, In the realignment step using RealignerTargetCreator and IndelRealigner, for tumor and normal pair, should they run this step separately or together using, e.g. -I tumor.bam -I normal.bam? Thanks,
View ArticleSNP calling using pooled RNA-seq data
Hello, First of all, thank you for your detailed best practice pipeline for SNP calling from RNA-seq data. I have pooled RNA seq data which I need to call SNP from. Each library consists of a pooled...
View ArticleFastaAlternateReferenceMaker generate a reference fasta rather than my sample...
Hi, I am using the following command, wanting to generate haplotype fasta for 97 samples: java -Xmx25g -jar $gatk -T FastaAlternateReferenceMaker -R $ref_genome -o new_output.fasta --variant $vcf Here...
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