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 … 

 

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. … 

 

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.

 

HaploGrep 2 Stand-alone Version

With some delay, we finally updated the stand-alone Version of HaploGrep to the latest version 2. This includes the latest Phylotree 17 (Forensic Science International: Genetics Supplement Series, from December 2015), finescaling the human phylogeny even further. This version has no file-upload limit as  currently applied on the web service (file size of 5MB and … 

 

New HaploGrep Exports in Detail

Here’s the overview of the new export options, HaploGrep 2 offers, by clicking on the small arrow next to Export: a) The HaploGrep result file as default format, ending with .HSD – find out more about the simple text-format, as well as an Example file. b) The extended HaploGrep result file, with remaining and not … 

 

Phylotree 17 available

After exactly 2 years, Phylotree, the “database” behind HaploGrep got updated by Mannis van Oven. Here’s the accompanying publication on Phylotree 17 . The mtDNA tree has now 5,437 haplogroups, which is a growth of over 13% to the previous version. Find out how Phylotree 17 differs for your dataset, by using the updated HaploGrep 2 … 

 

1000G Phase 3 mtDNA data available

The 1000 Genome Consortium recently released the Phase 3 mitochondrial DNA data of over 2,500 samples for download, besides their papers in Nature, stating: Mitochondrial chromosome variants are now available for the Phase 3 individuals from our FTP site Since in the current Version HaploGrep 2 can deal with the VCF file (unzipped), all 2500 …