Metadata for ComputeGCProfiles in GenomeSTRiP
Hi there, I'm trying to run ComputeGCProfiles from the GenomeSTRiP suite, but am running into a problem that seems to be related to the metadata. I am using the mouse mm10 genome and have built...
View ArticleCall variant from RNA-Seq data using Haplotypecaller
Hi My understanding is that Haplotypecaller is specifically designed to call variant from DNA-Seq data. However, RNA-Seq has different (more complicated) allele frequency. How comes that...
View Articleerror while running RealignerTargetCreator
Hello All I have sample obtain from Ion torrent machines I already did preprocessing of samples but when i am running RealignerTargetCreator its giving me error I am not able to tackle it please help...
View ArticleDepth of Coverage using overlapping windows
Hi GATK team, I am currently using the Depth of Coverage option for GATK for a precursor to detect CNVs. I had to specify intervals that did not overlap in order to get individual predictions for the...
View ArticleRankSum params
Hi, Why MQRankSum ReadPosRankSum is calculated for some variants but not all ? Below are 2 variants from same file. X 33032663 . A T 19668.77 PASS...
View ArticleBam not accepted by HaplotypeCaller
Hi there, Simulated some reads. My bam has around 400 reads.. trying to run haplotypecaller but getting error. Need help $ java -jar $GATK -T HaplotypeCaller -R ucsc.hg19.fasta -I pex_defaults_RG.bam...
View ArticleUsing Picard FilterSamReads with Java filters
I'm planning to use Picard FilterSamReads with FILTER=includeJavascript for some of my bamouts with --emitDroppedReads, and, to be frank, I still have no idea as for how that Javascript works. For...
View ArticleBug in HaplotypeCaller?
I was just running haplotype caller on a pool, and it gave an error message which (if I understand the options I gave it correctly) should not occur. My command was: nice -n 5 java -jar...
View ArticleSex specific SNP calling from pooled sample
hi. Can you guide me what specific parameters i should use if i want to make a sex specific SNP calling from a pooled samples of 50
View Articlecan VariantsToTable output the raw genotype call (i.e., 0/1) rather than the...
I'm interested in getting simple "heterozygous" or "homozygous" designations for all of the samples/SNPs in my multisample VCF file. In the past, I have been using the -GF GT option in VariantsToTable,...
View ArticleJoint Variant Calling and GenotypGVCFs on RNA-seq data
Hi! I was wondering how you guys are progressing with validating the joint sample genotyping workflow (specifically GenotypeGVCFs) on RNA-seq data, since I'm currently experiencing some errors in...
View ArticleVariantRecalibrator: Values for MQRankSum annotation not detected for ANY...
Hi, I am running gatk, I met some problems, please help me find the solution thank you. when I run HaplotypeCaller, I used the code like the following: java -Xmx2g -jar $GATK -T HaplotypeCaller -R...
View ArticleGATK / HaplotypeCaller and a genome w/ 250K references?
Hello, I am trying to understand what i'm seeing from HaplotypeCaller 3.6. I recently tried to use a genome build that includes the primary chromosomes plus ~250K unplaced contigs. When I run haplotype...
View ArticleInvalid sequence number 0 in index file
Hi, I've been using the RealignerTargetCreator tool with a pair of BAMs representing a tumor/normal pair to do joint indel realignment, and I get the following error message: ERROR -- ERROR stack trace...
View ArticleQuestion: RNAseqC: WARNING: Transcript has no coverage
Hello, I am working with a paired-end data set of rhesus macaque reads aligned with STAR against a current rhesus .fasta reference and .gtf annotation. I am interested in doing some quality control...
View ArticleRaising the heap size in the CNV discovery pipeline
Hi, I am trying to run the cnv discovery pipeline using the newest release of genomsetrip on ~400 bam files but I keep getting the following error at various locations of the pipeline, shown here for...
View Articleillustration about Resource Bundle
Hi, I encountered a problem when using PrintReads function in the stage of BQSR. The below is my command: java -Xmx4G -jar $jar -T PrintReads -R $ref -I $bamFil -BQSR $table -o $out Here the $ref is...
View ArticleCan Mutect2 be applied in tumor only mode for somatic variant detection?
I see in your documentation for Mutect2 you state: "MuTect2 currently only supports the calling of a single tumor-normal pair at a time" However, it appears to work in tumor only mode as well, at least...
View ArticleUsing CombineVariants to update GT fields with phasing information
Hi GATK Team I was wondering whether you guys have developed capability for updating GT fields with phasing information contained in another VCF? For instance, I generated phased genotypes using...
View ArticleMuTect2 output
MuTect2 gives only a vcf file as output. For MuTect, we have 4 files generated for each sample: B62047_N018_call_stats.out B62047_N018_coverage.wig.txt B62047_N018.vcf B62047_N018.vcf.idx I know how to...
View Article