FastqToSam error
Hi I am trying to generate bam files from reads (originally in fasta format) with ‘artifical Q-score’ generated with the attached script ‘fasta_to_fastq’ First step : I created fastq file from source...
View ArticleIndel Variant recalibration is showing an error
I have done joint genotyping of 200 samples and I have a multi sample vcf file. SNP recalibration worked but when I did Indel quality score recalibration it shows an error "MESSAGE: Bad input: Values...
View ArticleVariant is not called.
I have 2 BAM files generated by two different aligners which are NovoAlign and BWA. A screenshot can found in the attachment below showing that these 2 BAM files are the same at location 155900....
View ArticleGenotypeGVCFs --max_genotype_count not working?
Hi, I'm currently trying to call SNPs from a mixture of 42 pooled (a 10 individuas) and 50 individual sequenced chicken, using HaplotypeCaller and GenotypGVCFs (GATK3.7). Using the HaplotypeCaller, the...
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Variant calling inconsistencies using GVCF
Before starting, I'm a grad student without formal training in bioinformatics so I've mainly learned from online forums. That being said, if this question is stupid or I'm missing critical information,...
View ArticleIs Indel realignment removed from GATK4?
I am seeing help of GATK4 (hellbender), and for example for the tool ReadsPipelineSpark, it says, Takes aligned reads (likely from BWA) and runs MarkDuplicates and BQSR. The final result is...
View Articlebamout question
Hi , I am using GATK 3.7. Is it a true statement that bamout produce alignments only if there is variant found by haplotypecaller in given region ? Thanks,
View Article(howto) Recalibrate variant quality scores = run VQSR
Objective Recalibrate variant quality scores and produce a callset filtered for the desired levels of sensitivity and specificity. Prerequisites TBD Caveats This document provides a typical usage...
View ArticleGQ in BP_resolution VCF
I generate a vcf with bp resolution using following command with GATK 3.7 $ java -jar ~/Downloads/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19.fasta -I NA03403.bam -o...
View Articlepicard CrosscheckReadGroupFingerprints
Hello, In the picard CrosscheckReadGroupFingerprints command, it asks for a Haplotype_map file. What format does Haplotype_map file need to be in? If you have multiple BAM files with the same RG tag,...
View ArticleGATK runtime error: GenotypeGVCF
Hi, I was trying to use the GenotypeGVCFs tool on was data. I specify 8GB for heap (java -Xmx8g) and run the program but I get a runtime error. Is there something I should be doing differently? Also,...
View Articlepicard CalculateHsMetrics/CollectHsMetrics got stuck somewhere
I ran the following command java -Xmx130g -Xms80g -Djava.io.tmpdir=javatmp/ -jar ~/picard.jar CollectHsMetrics BAIT_INTERVALS=annotations/NexteraRapidCapture_Exome_Probes_v1.2.interval_list...
View Articlepseq loc-intersect
This is the most unfriendly software I have ever used, I am sorry to say this. but what are the refseq and locdb anyway!!!!!!!!!!! there is no any clear explanation, no where!!!!!!!! pseq ....
View ArticlemaxNumHaplotypesInPopulation
Hello! I am reading through the document for "HC step 2: Local re-assembly and haplotype determination" and have a question on the "maxNumHaplotypesInPopulation". For a given region, should the number...
View ArticleAre my data and research question appropriate for analysis with HaplotypeCaller?
Hello GATK team! I'm having a hard time finding discussion of and examples of use of HaplotypeCaller by researchers with similar data and research questions as me so apologies for posting on your forum...
View ArticleMutect 2 Hard Filters
Hello, In the Mutect 2 home page, you mention that there are some in-built hard filters: "MuTect2 also differs from the HaplotypeCaller in that it does apply some hard filters to variants before...
View ArticlePiccard tools error using CollectRnaSeqMetrics
Hi, I am attempting to use CollectRnaSeqMetrics from picard tools on my BAM files but I am not being successful with it for some reason. Below is the code that I am using: java -jar...
View ArticleGATK4 does not include DepthOfCoverage tool
It appears that DepthOfCoverage is not listed as a tool for GATK4, I get the following error A USER ERROR has occurred: 'DepthOfCoverage' is not a valid command. I have searched through the list of...
View ArticleRead group information required for MarkDuplicates?
I have 6 samples. The samples were multiplexed and run in multiple lanes on the same flowcell. I have not annotated the BAM files with any read group information. Is it okay if I just merge all BAM...
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Phred-scaled Quality Scores
You may have noticed that a lot of the scores that are output by the GATK are in Phred scale. The Phred scale was originally used to represent base quality scores emitted by the Phred program in the...
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