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!

 

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 … 

 

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 … 

 

HaploGrep 2.0 is ready!

Over the last years, HaploGrep became the de facto standard for automatic haplogroup classification (~ 18.000 users, cited over 140 times, about 120 local installations) and is also used in several commercial systems and research pipelines. There was quite some work done underneath the surface of HaploGrep, especially to improve our haplogroup classification performance and … 

 

Importing VCF file to HaploGrep 2.0

With the establishment of NGS-Devices and the resulting data flood, new file formats such as FASTQ, SAM, BAM or VCF became de-facto standards in the bioinformatics data world. Especially the VCF-file containing the variants became of special interest in the user requests lately.┬áThere are some python scripts available, that convert a VCF file to a …