0/1 alleles in
My phased file contains alleles called 0 and 1 which are defined in files beagle site provided (e.g. ALL.chr1.phase1_release_v3.20101123.filt.int), so I'm getting an error: Illegal base [0] seen in the...
View ArticleHow read groups affect Variant Calling?
Hi, I have a bam file with multiple read groups for same sample. Does variant calling algorithm (UnifiedGenotyper) will consider bam file as multiple-sample data or a single sample-data (irrespective...
View ArticleCan I use GATK to select a private SNP from multi sample VCF file
Can I use GATK to select a private SNP from multi sample VCF file? With a private SNP I mean a SNP where all but 1 sample in a multi sample vcf file are genotype 0/0.
View ArticleHow to transpose the results of Depth-of-Coverage?
I use the GATK Depth-of-Coverage function output for multiple samples below. but when I open the output file, I found the format is transponse as what I want. I wants the output file row: capture...
View Articlevariant to table
I'm trying to take a merged vcf file and output counts of homo/het to a table using Variants to Table. the tables are not anyway the same length as the vcfs that I am creating them from. Is there any...
View ArticleRunning with Queue?
Dear developer of XHMM, I wonder is it possible to integrate the XHMM into GATK so people can run it with Queue? And How to do it? Thanks!
View ArticleAsk your questions about XHMM here
The author of XHMM will respond to questions posed in this section. You can also comment on the articles in the "XHMM Documentation" subcategory. Please don't post your question as a new comment on...
View ArticleAll GATK DoC files must have the same targets
I splited up my samples into two groups. since one set had a different Target Exome; to combine GATK Depth-of-Coverage outputs, I used mergeGATKdepths commands, and I got this error. All GATK DoC files...
View ArticleERROR: Cannot find ':' in target string chr1
I am at the stage of mean-centering the target after filtering samples and targets. I got this error ERROR: Cannot find ':' in target string chr1 from the following code...
View Articleevaluating xhmm performance
We have a set of exome files which we estimate CNV using XHMM. In the other hand. we have CNV of the same individual samples using Agilent 1M. Would be great if you elaborate a little bit, what is the...
View ArticleUnsuccessful XHMM run
Good day I have run the XHMM pipeline in in order to ID CNV's from 9 sample exome sequences. Unfortunately the .vcf file was empty. I assume this may either mean that there are no CN variants within...
View ArticleERROR: Cannot find ':' in target string total_coverage
Running xhmm to "Filters samples and targets and then mean-centers the targets" as follows results in the error posted in the question. Not sure what this is referring to? xhmm --matrix -r...
View Articlepredicted CNV for a patients with both X and Y chromosome
In am looking at the CNV output and it seems for a patient, CNVs are predicted on both X and Y chromosome ! how should I interpret that. Also, I am curious to know, if there is already an script to...
View ArticleEXOME.interval_list
Hi Menachem, I followed the workflow at "https://atgu.mgh.harvard.edu/xhmm/tutorial.shtml" for XHMM and I am planning to use XHMM for an Exome project with 60 Samples. This is a question just to make...
View Articleinterval_list_to_pseq_reg
Hi Menachem, Following the workflow I got an error running "interval_list_to_pseq_reg" ./sources/scripts/interval_list_to_pseq_reg EXOME.interval_list > ./EXOME.targets.reg Error: awk: line 4:...
View ArticleLength of time to complete DepthOfCoverage?
I'm on the first step in the xhmm pipeline, which involves running my .bam files into DepthOfCoverage. I have 13 bam files (1 for each exome) and it ran out of memory (8gb) per core (10 cores) after 40...
View ArticleParameter adaptation for Panel sequencing
Hi everybody, when working with sequencing panels such as TruSight One, do you have to change some default XHMM parameters especially in the HMM params.txt file? Thanks, Christian
View ArticleWhy the format field is different between variant sites and homo-ref sites?
I was trying to extract genotype for every sample, including sites where the MAF doesn't pass the minimal threshold, by setting output_mode EMIT_ALL_CONFIDENT_SITES. Especially, I am curious about the...
View ArticleCan xhmm be used with whole genome sequencing data?
Can xhmm be used with whole genome sequencing data? if not which tools are available for cnv analysis using whole genome sequencing data. thanks Saad
View ArticleHow XHMM work
Hi @fromer I am interested in how xhmm work.The paper tells much about the pre-processing steps, but little about how hmm step work with the input parameters.I am wondering if there is any detailed...
View ArticleTrain once, predict many times.
Hi, I have spent some days playing around with XHMM, and I have managed to follow and reproduce the output in the tutorial. However, I am still not sure whether XHMM is the right tool for my task at...
View ArticleCould not read any samples from GATK depthcoverage file.
I have two sets of depth coverage file from GATK 2.5-2 and would like to merge them. however, I am facing the following error. ERROR: Could not read any samples from...
View ArticleCalling a deletion as a duplication
I was able to get through the xhmm pipeline without any drama! Unfortunately, I ran into a problem where multiple people in a family have a deletion in a certain region, and some people in the family...
View ArticlePLINK/Seq tools and some errors.
Hi! I'm trying to use XHMM for CNV detection but I have a few problems: 1) I'm following this quide http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml for the use and I installed PLINK/Seq tools but when...
View ArticleXHMM support is no longer available here
For XHMM support, please go to http://atgu.mgh.harvard.edu/xhmm/questions.shtml
View Article