variantRecalibrator-command not found
Dear all, After I used vctutils.pl to filter the SNPs, Im trying to run variantRecalibrator to recalibrate the SNPs. I run the command line as follow: java -Xmx4g -jar...
View ArticleGATK Base Quality Score Recalibration -- Do I need .after_recal.table ?
This is what I have in my pipeline to do base quality score recalibration, and I got this from the best practice for GATK from GATK website: java -Xmx50G -Djava.io.tmpdir=tmp -jar ${GATK} -T...
View ArticlePicard IlluminaBasecallsToSam: LIBRARY_PARAM file does not have column...
Hi, I am following the GATK pipeline and after running Picard CheckIlluminaDirectory and ExtractIlluminaBarcodes successfully, I encounter a problem to generate the BAM files with Illumina...
View ArticleUsing Pipes for BWA Picard tools
I found that if I use named pipes for preprocessing fastq data with BWA and Picard, it saves more than 1/3 time. To use named pipes for picard, I must give the name for each output with .sam, this way,...
View ArticleOutputting bamout to read post-realignment coverage including non-variants
Hi, I want to output a bamout to see the post-realignment coverage (a la -A DepthPerAlleleBySample) for a position, regardless of whether that site is a variant site. I'm sure I'm need to turn on...
View Articlemutect call error:java.lang.NumberFormatException: For input string: "R"
Got a java error running mutect: java.lang.NumberFormatException: For input string: "R" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at...
View ArticleIs there a way to remove the "|" from the SQ line in a .bam file?
We have several, unique H. pylori genomes. We have aligned each of them to a reference genome, which had "|"in the fasta (or .fa) file name. Now, when running through GATK, we cannot create our final...
View Articlesamtobam after Bowtie2 alignment
Hello, I did my alignment to a reference genome using Bowtie2. I used paired end and unpaired sequences in doing so. Then I used view from samtools to convert my sam files to bam files. During the...
View ArticleWhy does GATK LeftAlignAndTrimVariants set a missing genotype to 0/0?
Hi. I appreciate many your helps. I have one vcf file (a.vcf). This file has one variant data. The data also has missing genotypes "./." because of DP=0. The variant is tri-allelic variant as below....
View ArticleBug in output VariantFiltration with --genotypeFilterExpression
When using VariantFilteration with genotype filters, the FORMAT line for the genotype filter is wrong: ##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype-level filter"> It should have...
View ArticleAlternative basecallers with GATK?
Hi! We are working on various non-model organisms without snp databases available. Of course this makes BQSR a problem, and we're not entirely convinced by the "bootstrapping" method. However the...
View ArticleHow to change @SQ file in a .bam file
I am trying to run GATK to get a g.vcf file using an interval list. I get the following message: ERROR MESSAGE: File associated with name interval.list is malformed: Interval file could not be parsed...
View ArticleThe -allSites option in GenotypeGVCFs did not emit every position
I was using the -allSites option in GenotypeGVCFs with 100 samples. I found that many positions were missing in the combined gvcf even though these positions have well-supported reference call in every...
View ArticleGATK HTC snp events at adjacent bases
I concurrently used haplotypecaller and samtools mpileup for calling phase events on exome data. In certain edge-cases I found that if the SNPs are on adjacent residues, HTC treats them as two separate...
View Article(howto) Test your Queue installation
Objective Test that Queue is correctly installed, and that the supporting tools like Java are in your path. Prerequisites Basic familiarity with the command-line environment Understand what is a PATH...
View ArticleGatk Variantannotator not reannotating old rsIDs
Hello Everyone, I am trying to reannotate some .vcf produced using the miSeq pipeline using dbSNP version 137. I am currently using VariantAnnotator to reannotate the called variants with the latest...
View Articlemultiplexed sequencing and multi-library designs
sorry, just a confusion, whether does generating many independent leukemias from one ”founder” mouse mean I need to pre-process my data from multiplexed sequencing and multi-library designs or can...
View ArticleLocal Realignment around Indels
For a discussion of the implications of removing indel realignment from workflows, see Blog#7847 from June 2016. Realigner Target Creator For a complete, detailed argument reference, refer to the GATK...
View ArticleStrange bamout output
Could anybody explain what shows in the figure? why the length of reads from bamout is 40 or 60? Why there is no coverage at all part of exon? How to explain the difference between the output from BWA...
View ArticleWarning message from VariantDataManager
Hello, I notice the following warning messages during the first step of VQSR: ------------------------------------------------------------------------------------------ Done. There were 3 WARN...
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