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Gregor-Mendel-Institute/SNPmatch
Link to database is incorrect

Dear, Thanks for your tool. Sadly the link to the SNP database for the 1001genome project doesn t work. In the main page it is said that we can download from https://gmioncloud-my.sharepoint.com/personal/uemit_seren_gmi_oeaw_ac_at/_layouts/15/guestaccess.aspx?folderid=0ca806e676c154094992a9e89e5341d43 ...
  • JoseMMuino
  • 1
  • Opened 
    on Sep 26, 2022
  • #19

Gregor-Mendel-Institute/SNPmatch
Error when providing data without PL

Hi, I was testing the program but I get an error when parsing data that does not contain PL (either VCF file without PL or bed format). To check if it was my input file I tried out with the provided bed ...
  • dovivi
  • 1
  • Opened 
    on Aug 31, 2022
  • #18

Gregor-Mendel-Institute/SNPmatch
Incongruities at program results

Hello, im using SNPmatch in a VCF file where i have 7 replicates of 3 different plants (21 samples in total), i made the database with them and then i splitted in 21 separated VCFs to run the program with ...
question
  • dukelheit
  • 3
  • Opened 
    on Sep 26, 2020
  • #17

Gregor-Mendel-Institute/SNPmatch
An error occurs while using recommended version of scikit-allel (0.20.3)

After installing snpmatch using the recommended conda enviroment i had tried running it with the next code: snpmatch inbred -d all_chromosomes_binary.hdf5 -e all_chromosomes_binary.acc.hdf5 -i 701_501.filter.vcf ...
  • dukelheit
  • 1
  • Opened 
    on Jul 16, 2020
  • #16

Gregor-Mendel-Institute/SNPmatch
Problem with chr names are sorted by default in np.unique

  • rbpisupati
  • Opened 
    on Jul 14, 2020
  • #15

Gregor-Mendel-Institute/SNPmatch
Generalize genotype_cross based on chromosome names in input

  • rbpisupati
  • Opened 
    on Jun 5, 2019
  • #14

Gregor-Mendel-Institute/SNPmatch
Different results when input is shuffled

I have installed SNPmatch using docker-miniconda and created several tests. If you want more information, I can provide all the steps I used to produce the examples below. For now, I will just show the ...
  • davetang
  • 5
  • Opened 
    on May 30, 2019
  • #13

Gregor-Mendel-Institute/SNPmatch
Parsing VCF files filters out non integer Chromosomes

genotypedata db does have all the information
  • rbpisupati
  • Opened 
    on Aug 10, 2018
  • #12

Gregor-Mendel-Institute/SNPmatch
TypeError in JSON file output of genotyper inbred

Here is the detailed error, Traceback (most recent call last): File /mygit/SNPmatch/snpmatch/__init__.py , line 191, in main args[ func ](args) File /mygit/SNPmatch/snpmatch/__init__.py , line ...
  • rbpisupati
  • Opened 
    on Aug 10, 2018
  • #11

Gregor-Mendel-Institute/SNPmatch
error when using snpmatch, throw error if bcftools doesnt exist in the path

Hello Mr. Rahul, I am Vinay, a master student from University of Hohenheim, i decided to use snpmatch as a propability test check my master thesis samples of maize with related original varieties from ...
enhancement
  • vinay104
  • 21
  • Opened 
    on Aug 8, 2018
  • #10
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