VariantRecalibration step issue
Hi all, i need some advice about VariantRecalibration as in if I am doing the right thing? Downloaded 30 bams from 1000 genomes and realigned them to HG38. Then using HaplotypeCaller generated a gVCF...
View Articlepreprocessing raw sequence data in a UBAM file from IonTorrent 16S...
Hi everyone! I have raw, paired-end sequence data in a UBAM (unmapped) file after sequencing 16S gene from water samples. The UBAM file contains both forward and reverse reads but unjoined. How can I...
View Articleextracting forward and reverse reads from uBAM file
Hi everyone, I am using Ion 16s Metagenomics kit to perform microbiome analysis in wastewater. After performing paired-end sequencing, I have been given raw reads in a UBAM file which contains both...
View ArticleReadsPipelineSpark Error: reference and reads have incompatible contigs
When running the ReadsPipelineSpark (4.0.1.2) with the align option, a USER ERROR regarding inconpatible contigs is generated. However, the input bam file has no contigs as it is an unmapped ubam...
View ArticleDuplicate records after CalculateGenotypePosteriors
Hi, I follow this thread to execute results from a trio but I discover there are many duplicate records after CalculateGenotypePosteriors. Code brief describe here: java -Xmx16g -jar...
View ArticleAllelic Coverage Pulldown at genomic loci
Is there a GATK tool that can pull down the allelic coverage at a site in the genome for all alleles? The output format I'm imaging is (A,C,T,G) counts for each genomic loci I specify. Can someone...
View ArticleVariantsToTable - all fields
Hi, Can the VariantsToTable walker produce output containing all the fields in the VCF without you having to specify them in the command? Thanks Kath
View ArticleVariantRecalibrator - no data found
I just updated to the latest nightly and got the same error: INFO 12:03:16,652 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00258 INFO 12:03:23,474...
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GATK4 VariantAnnotator
Hello, Has this tools been removed in the last release ? Thanks, Pedro
View ArticleReadBackedPhasing of somatic and germline variants?
Hi all, I'd like to know which germline variants are proximal to and on the same chromosome as detected somatic variants. Is there an out-of-the-box way to phase germline and somatic variants to one...
View Articlehard filtering one WGS raw.g.vcf
Hi, Im trying to apply hard filter to one WGS.g.vcf (coming form HaplotypeCaller). The command im using is: java -jar ${GATK}/GenomeAnalysisTK.jar -R ${reference}/mm10.fa -T SelectVariants -V...
View ArticleWhy I obtained a g.vcf with wrong variant DPs, and too few variants according...
Hi, I extracted Exome regions from public bam files to apply the same pipeline that I did for my samples and merge them. It is weird that looking in the g.vcf files, I have very few "variants", and...
View Article[PICARD] CollectInsertSizeMetrics vs CollectAlignmentSummaryMetrics
Hello, I am getting some confusing results and not sure how to explain them. I am interested in the total number of reads from a PE library that actually mapped to our reference so we can take that...
View ArticleMouse Genocode version 15 bindle file
Dear GATK team, I am looking for mouse genome bundle file in order to use BQSR. I found this link on search ftp://ftp-mouse.sanger.ac.uk/current_indels/. Do you think i can use this? and is it...
View ArticleGatherBamFiles / FixMateInformation / ValidateSamFile
Hi, here the pipe... 1) ApplyBQSR while read -r f1 f2; do .... ${ph6} --java-options ${java_opt1} ApplyBQSR -R ${gnm} -I ${fBAM} -O ${fol5}/${c_applybqsr} -L ${f1} -bqsr ${fol5}/${bqsrrd}...
View Articleoverlapping read pairs in GATK 4.0.1.2
Hi, I came across this post regarding overlapping read pair: https://gatkforums.broadinstitute.org/gatk/discussion/1745/does-unifiedgenotyper-count-overlapping-paired-end-reads-as-two-separate-reads I...
View Articlerunning haplotypeCaller using Queue
I wrote my first script in scala to run haplotyperCaller walker of GATK. However, I am running into some errors when I execute the *.scala script. I am unable to figure out the source of error, any...
View ArticleHow does the BwaSpark in GATK4 control the number of threads?
I tried to ERR000589 process data with BwaSpark. The bam file size is 1.3G. The average time spent is about 25 min (5 nodes). However it would only cost 5 min in processing same data if I tried to use...
View Article[GATK 4.0.1.2] unsorted bam in mutect pipeline running in tumor-only mode...
Hello, I need your help on using Mutect2. I tried to call somatic mutations using mutect2_multi_sample.wdl in tumor-only mode with make_bamout = true and scatter_count = 50. It was failed for a small...
View ArticleMissing field QD in vc variant (ERROR)
Hello! I'm trying to extract SNPs of interest from my filtered VCF file of passing SNPs. I just used SelectVariants to create that file, and am now trying to use VariantsToTable to put them into a...
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