haplogrep-cmd
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seppinho
HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
I would like to use HaploGrep to classify a FASTA sample with respect to the RSRS, but the option does not seem to work. I get the error: `[classify, --in,...
i want to get the sample quality and HG quality in addition to overal quality using command line haplogrep. how can get these results in output file using command line?
Hello，when I run haplogrep in Linux, I will meet an exception. ''''' mtDNA Haplogroup Classifiction v2.4.0 https://github.com/seppinho/haplogrep-cmd (c) Sebastian Schönherr, Hansi Weissensteiner, Lukas Forer, Dominic Pacher [email protected] [classify, --in, /lustre/wangzh/mtDNA/genebank/sample/AB055387.1.fasta,...
Hi, I have created a merged vcf file using **vcf-merge** tool for ~1000 samples. When I am trying to provide this file as an input for the haplogrep, it is...
Hello, I am using VCF files (created by Mutect) as input for haplogrep2 and I am having issues with processing indels, which are longer than 1-bp. I had to change...
Dear all, Is it possible to run haplogrep2 on non-human species to identify haplogroups? If not, what additional information would I need if I wanted to set this up on...
The table is result of my haplogrep2 Quality score and some quality score >1 ，Is this situation right？ Rank | Quality | Not_Found_Polys -- | -- | -- 1 |...
The feature released in 497cf6c13e23a7802eee5c3a96d07b855bff3119 in response to #12 allows for the export of the best _n_ haplogroups. When running with microarray data using the `--chip` flag, often there are...
As described in the README, the `--chip` flag will limit the range to array SNPs only. How are missing genotypes handled in a multisample VCF file? For example, my multisample...