Haplocheck: Contamination Detection in mtDNA and whole-genome sequencing studies

Today we are happy to announce haplocheck, our approach to detect contamination in mtDNA and even in whole-genome sequencing studies. By analysing only the small 17Kb mitochondrial genome (included as a by-product in each whole-genome sequencing run) haplocheck can be used as a fast proxy tool to estimate contamination. Therefore, only a fraction of the … 

 

HaploGrep2 Update 2.1.21

With HaploGrep version 2.1.21 the handling of human mitochondrial FASTA sequences gets a new improvement. As we use BWA 07.17 for the alignment of FASTA sequences, the mtDNA nomenclature is not always met by default. Therefore we provide a new parameter which will fix the nomenclature to the correct one used in Phylotree, finally yielding a … 

 

Score calculation in HaploGrep

In this blog post we show how Haplogrep’s default measure (so called Kulczynski measure) works on a concrete example. (Note: this blog post has been updated after receiving a correction from Chris Simpson, Thanks!) So let’s say this is your input sample in hsd format: test 16024-16569;1-576; ? 73G 263G 285T 315.1C 455.1T 523G 524T … 

 

HaploGrep on GitHub

We’re happy to announce that the command-line version of HaploGrep is finally on GitHub. Due to increasing user requests over the last months, we also started a Google User Group to learn about your needs. Feel free to contact us if you have any questions. Happy Haplogrouping! HaploGrep on GitHub

 

Errors and Warnings in HaploGrep2

What triggers an Error and what is considered a Warning in HaploGrep2? Here’s a short overview of the events: Errors: The detected haplogroup quality is low. Sample is marked red. Quality <=80% The expected haplogroup is not a super group of the detected haplogroup Common rCRS polymorphism not found! The sample seems not properly aligned to rCRS. … 

 

HaploGrep Rest API

Simple Rest API is up and working again. Please check this article for further details. Best. Sebastian

 

HaploGrep2 Update 2.1.1

2 haplogoups were labeled wrong and are fixed now – thanks Rocio for pointing out! previously until 2.1.0 correct in 2.1.1 R0+16189 R+16189 H+16311 HV+16311  

 

Combine multiple VCF files

HaploGrep2 currently accepts only single file uploads. To merge several VCF files to one, several tools exist: CombineVariants vcfcombine vcf-merge An example based on the VCFtools can be found here: # For each VCF file: bgzip Variants_sample_A.raw.vcf tabix -p vcf Variants_sample_A.raw.vcf.gz vcf-merge *.raw.vcf.gz >| Variants_all_samples.raw.vcf Hope this helps!

 

HaploGrep2 Update 2.1.0

We just updated HaploGrep2, with the following minor points: the Export of the Extended Report (Export / Haplogroup Extendet (txt)) got extended with the “Found_Polys” – see Describtion below: The Report for the potential Phantom Mutations got corrected, so that positions with bases according the rCRS reference are not listed anymore. Report of the possible … 

 

HaploGrep2 publication

Happy to announce the publication of the HaploGrep2 paper in this years Web Server Issue 2016 in Nucleic Acids Research. For data generated with massive parallel sequencing devices in form of fastq or bam files, the mtDNA-Server paper also published in this years issue, gives some details there.