Ploidy level in HaplotypeCaller in GATK 4.0
Hi, Thanks for the new version of GATK (GATK4.0). We have a pooling of 48 samples and the organism is diploid, we are using ploidy of 96 (48x2=96). earlier when I am using HaplotypeCaller for variant...
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GATK4.0.0.0 HCspark step run on spark cluster, -Unable to find _SUCCESS file
hello l tried to use the latest GATK version 4.0.0.0 on spark cluter,this step is HCspark .but I meet the question as follow the picture but when i can find it in my hdfs system,the result as follow...
View ArticleIndelRealignment step: Lost of reads?
I'm using IndelRealigner tool on my BAM file and then counting the number of reads in the BAM file using samtools stats and it turns out that in my input BAM I have 167170574 reads mapped while in the...
View ArticleValues for indel qualities
Hi, I am a researcher from the Politecnico di Milano. I would like to ask a clarification about the indel qualities transition probabilites of the PairHMM in HaplotypeCaller. I am using some of your...
View ArticlePicard Sort Vcf Error
Hello. I am using GATK version 3.6, picard-2.8.2.jar I downloaded hapmap_3.3.hg38.vcf from gatk resource bundle. I then used the below command to remove chr notation. awk '{gsub(/^chr/,""); print}'...
View ArticleIs GATK4 HaplotypeCaller in evaluation phase?
Hi GATK team, Congratulations on the release! I just found this public method in FireCloud that notes that HaplotypeCaller in GATK4 should not be used for production use yet since it is still in...
View ArticleFilterSAMReads ReadID pattern in Read_LIST_FILE
Hello, I am running FilterSamReads in picardtools with the following command: java -jar /bioinf/software/picard/picard-1.133/picard.jar FilterSamReads...
View ArticleMuTect2 and smalls mpileup reads info seem to be very different?
Hi - I used MuTect2 to call variants in multiple samples from one patient. However, I wanted read information for those samples where a mutation wasn't detected in all the samples and decided to use...
View Article-nct not present in GATK 4.0.0.0
Hi, Is --native-pair-hmm-threads in GATK 4.0.0.0 same as -nct in older GATK versions?
View ArticlePlease help for the very beginer--cannot build GATK4
Hello, I am very new unix learner. I use bash on Ubuntu on Windows10 I have downloaded and unzipped GATK-4.0.1.1, and gradle wrapper (latest version), java version:openJDK 1.8 when I run ./gradlew in...
View ArticleQuestions about GenotypeVCFs output
Hi, I generated 12 .g.vcf files with HaplotypeCaller in GVCF mode and then a vcf with GenotypeGVCFs. What's the easiest way to split this vcf per sample ? Should I apply hard filtering first and then...
View ArticleAbout SelectVariants
I want to filter out the variants if VAF in tumor samples was more than 0.3. Command line: gatk SelectVariants -V somatic_twofiltered.vcf -R ucsc.hg19.fasta -select...
View ArticleWhere to find CreateSequenceDictionary.jar?
I've downloaded the recent GATK 3.7-0 release, which does not include CreateSequenceDictionary.jar. Is the following command replaced by something new? java -jar CreateSequenceDictionary.jar R=...
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 Articleno. of cores utilization in haplotypcaller in GVCF mode
Hi, I am running Haplotypecaller (v4.0.1.2) (not the spark version) on some WGS samples on a SGE (Sun grid Engine) cluster. When I am submitting a job to my cluster, I am asking for 1 core (on an 8...
View ArticleAF in vcf files
There is some inconsistency in the community on how to calculate the AF (allele frequency) value in vcf files. GATK calculates a hypothetical value (0, 0.5 or 1 for normal diploid organisms). Other...
View ArticleHow can I exclude multi-mapped reads before using UnifiedGenotyper to call SNPs
Hi, how can I exclude multi-mapped reads before using UnifiedGenotyper to call SNPs? You mentioned picard that could be used to exclude multi-mapped reads. However, which tool of picard should be used?...
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Variant calls in mixed samples - HaplotypeCaller GVCF
I have a question about the behavior of HaplotypeCaller when used incorrectly Specifically, how would it call variants from a diploid sequence if the ploidy was set to 1? Would it simply call the most...
View ArticleRealignerTargetCreator hangs
Hi GATK team! we have an issue with running the RealignerTargetCreator unfortunately. Commandline looks like this: gatk -T RealignerTargetCreator -R ref.fasta -I /testsample.sorted.bam -nt 32 -o...
View ArticleHow can I exclude multi-mapped reads before using UnifiedGenotyper to call SNPs
Hi, how can I exclude multi-mapped reads before using UnifiedGenotyper to call SNPs? You mentioned picard that could be used to exclude multi-mapped reads. However, which tool of picard should be used?...
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