joint calling and hard filtration
Hi there, I have vcf file with mutiple samples. I have to do hard filtration because in have limited samples and size i am looking into. What is the recommendation - 1.should i split file per sample...
View ArticlecombineGVCF batch effects
Dear Sir/Madam, We have been using the best practice variant calling pipeline to call variants in our targeted sequencing data (GATK 3.2.2). Me and others in the team have discovered batch effects in...
View Article"ERROR MESSAGE: Rod span 1:1-249250621 isn't contained..." while running the...
When I try to run the HaplotypeCaller I get this error below. Although I have searched the forum and elsewhere for solutions, I cannot solve the issue. I get "No Errors found" when I run picard.jar...
View ArticleBQSR: Is it safe to use run_without_dbsnp_potentially_ruining_quality in this...
In this particular situation, after calling variants using a genome assembly reference, we would also want to see where there are any variations accumulated in the reporter vector, and as such the...
View ArticleSomehow the requested coordinate is not covered by the read?
I was running some samtools calls through UG with genotyping_mode GENOTYPE_GIVEN_ALLELES after reading this thread:...
View ArticleUsing previously processed WXS BAM file
Hi, I have received some cancer patient derived xenograft sampleb WXS data as BAM files that seem to have been partially processed through the GATK pipeline. Based on the header information it appears...
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...
View Articlerules for max_alternate_alleles in HaplotypeCaller
Hi, I can't come to any clear conclusion how this parameter works. Help me, please. I worked on the same files with exact command but the max_alternate_alleles. In first command I put 1 for its...
View ArticleGATK vs MuTect2
first question, which is better to use on unmatched cancer samples (no normal panel either), MuTect or GATK? second, I ran GATK on two samples (pair), for which there was a different list of mutations....
View ArticleGenotypeGVCFs and annotation for VQSR
Hello, I want to combine 60 genomes with genotypeGVFs to perform VQSR according to your best pratice But I would like to know if I should recompute annotation or if it is automaticly perform. I want to...
View ArticleHow MuTect filters candidate mutations
Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to...
View ArticleAlternate Alleles in VCF are more than 1 base
Hi there, I've removed INDELS from a multi-sample vcf from HaplotypeCaller using SelectVariants. However, the ALT 'SNPs' are more than a single nucleotide substitution. Eg....
View ArticleHaplotyper memory issue
Hi. I am running Haplotyper with the below command. java -jar /usr/local/lib/GenomeAnalysisTK.jar -T HaplotypeCaller -R /media/data1/02_SNP_flanking_GC_content/am45new.fasta -nct 1 -I...
View ArticleGenotypeGVCFS gives fewer samples than input.
Hi everyone, I ran GenotypeGVCFs with the following command java -Xmx$64g -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R --variant 08_22_2016_murat5.list --dbsnp dbsnp_144.hg38.vcf.gz -o...
View Articlefilter clustered_events in Mutect2
Hi What parameter on Mutect2 command line can i use to "loosen up" the filter "clustered_events"? Thanks Severine
View ArticleHaplotype caller handling paired-end reads
Hi GATK team. I have some questions regarding on haplotype caller. I saw the forums and know that haplotypecaller does handle paired-end reads. But I can't find a parameter to claim that my data are...
View ArticleWhat is the output of MuTect and how should I interpret it?
Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to...
View Articlefraction_contamination and unrelated status
Hello, I recently used ASCAT to calculate percent contamination in a tumor specimen. I used array data to do this. I was also planning on checking this with contEst if I can get my SNP array calls into...
View ArticleI have downloaded GATK3.6 on my MAC however it seems an error that it cannot...
I have downloaded GATK3.6 on my MAC however it seems an error that it cannot be launched. What should I do?
View Article[Co-realignment] Somatic variant discovery (Cancer-specific processing)
I can't found the detail information of Co-realignment except for attached image. Could I get the improvment information of Co-realignment or detailed information? Can I processing the one BAM file...
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