VariantRecalibrator - 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...
View ArticleCan HaplotypeCaller be used on drug treated samples?
Hello, I am working on a RNASeq data which consists of liver samples from donors. It is a case-control study where 12 samples are divided as Normal (control) and Rifampin Treated (case). I want to...
View ArticleHouston Texans versus Cincinnati Bengals
NFL**Houston Texans versus Cincinnati Bengals | Reside Sports GameSeptember 18, 2017 through Thank you for visiting Nowadays American footbal ,Thurs . evening,Are living Houston as opposed to...
View ArticleDangling heads and tails
Hello, The logic for merging dangling tails appears to be different from that for dangling heads. For example, it looks like tails can be merged to a non-reference path while heads cannot. Is there a...
View Articlehow to create pon vcf
Dear GATK staff, I was trying to make a normal vcf file using GATK-4. However, there's no clear information about how to do that and could you show me the command line on how to create vcf files and...
View Articlepicard 2.10.7 fails pipelining SortSam and SetNmAndUqTags
Hi. I just upgraded to picard 2.10.7 and doing my regular exome work however I noticed this problem under 2 different platforms. 18:12:17.734 INFO NativeLibraryLoader - Loading libgkl_compression.dylib...
View ArticleJava error with -L in GATK v4.0.0.0 on win7 using Cygwin
I'm a happy user of GATK v3.7 running on a Win7 pc via Cygwin. With v3.7 it was no problem to use the -L (--intervals) option. Today I was trying the new v4.0.0.0 but ran into the following error:...
View ArticleErrors about input files having missing or incompatible contigs
These errors occur when the names or sizes of contigs don't match between input files. This is a classic problem that typically happens when you get some files from collaborators, you try to use them...
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Errors in SAM/BAM files can be diagnosed with ValidateSamFile
The problem You're trying to run a GATK or Picard tool that operates on a SAM or BAM file, and getting some cryptic error that doesn't clearly tell you what's wrong. Bits of the stack trace (the pile...
View ArticleAllele Depth (AD) is lower than expected
The problem: You're trying to evaluate the support for a particular call, but the numbers in the DP (total depth) and AD (allele depth) fields aren't making any sense. For example, the sum of all the...
View ArticleCallableLoci replacement in GATK4?
I noticed that CallableLoci does not exist in GATK4 anymore, is there a replacement tool for it in GAKT4? Thanks, Luobin
View ArticleWhere can I find the old format of best practices from GATK?
There was link for best practices which has a links to whole genome, whole exome SNVs and CNVs? Which details each steps in different workflows?
View ArticleGATK 3.8 Best Practice documents?
Hi there, Congrats on the version 4 release. Now the page are updated to 4 but I'm currently still working on 3.8, is there a link I can find the old best practice documents? Wenfu
View ArticleConvert CombineVariant output to individual vcf files
HI, I was curious if it possible to convert the output of CombineVariants back into individual sample vcf files. Based on answered questions in other threads, I am under the impression that you should...
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GQX values in gvcf
I found this description of the GQX value that is potentially available in a gvcf on the illumina website. The description implies this could be used to filter fairly/equally the variant and nonvariant...
View Article"Could not open array genomicsdb_array at workspace" from GenotypeGVCFs in...
I experience Issues with GenotypeGVCFs and GenomicsDB input in the final GATK4 release using the official Docker image. This does not occur using the 4.beta.6 release. It looks like there has been a...
View ArticleHaplotypeCaller 4.beta.6 gVCF performance
Hi, ever since the 4.beta.4 release, I've noticed a significant increase in the memory requirements and execution time of HaplotypeCaller in gVCF mode. I tested the 4.beta.2 and 4.beta.6 version of...
View ArticleOutlook on Grch38/hg38 for in exome and other targeted sequencing
Dear GATK team, First of all, congratulations on releasing GATK4! I was wondering, on this page: https://software.broadinstitute.org/gatk/download/bundle it is mentioned that the human genome reference...
View ArticleHas VariantAnnotator tool been removed from GATK
Hello, I am trying to run the following command with GATK 3-.8 without success. Has this tool been disabled? Thanks srun java -Xmx"$MEM"g -jar $GATK \ -R "$REFERENCE" \ -T VariantAnnotator \ --variant...
View ArticleGATK version 3.8 download
Can anyone send me a link to the GATK version 3.8 download? The link on the home page takes you to the download of 4.0 (even though it still reads 3.8). 3.8 is not listed in the archived versions either.
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