Hi all,
Is there a way to convert from SNP VCF format (obtained from GATK pipeline) into HapMap genotype format? I've got VCF files that I want to analyse with a program that requires HapMap genotype format. Any suggestions will be greatly appreciated! Thanks.
En-Hua Xia
you can download something called vcftools which is a perl script to convert text files to different formats.
Hi Sara, thanks for your reply. Could you give me a detail command line? I couldn't find any option of vcftools used for this conversion.
All the best,
En-Hua
Hi En-Hua Xia. In fact, if you can swith to plink hapmap format you can use the vcftools software and type vcftools --vcf --plink --out
But if you want hapmap 2 format then you have to use a custom script. I have made one that I can share if you still need it.
All the best.
Jean-Luc
hi En-Hua,
You can directly open vcf file in TASSEL software and export it in the hapmap file format easily. I have attached a doc file for more help.
@Apoorv Tiwari, many thanks for your kindly help and I will try it later.
@Apporv Tiwari, thank you very much for your great help and I will try this sure
@Jean-Luc Legras, could you please share the custom script?
Thanks,
Shamima
Hello Shamina
Here is my script. I used it to prepare data files for variscan. It is done for not too big files as it read the file first and then output it . I have added a parameter in case there is a requirement for an ancestral allele. In case this does not work, please tell me.
Now I have moved to PopGenome for my genetic test that accepts vcf files.
Best regards.
Jean-Luc
@Jean-Luc Legras, could you please tell me this perl script is written using BioPerl or Perl installation in linux ?
Looking forward to your answer.
Shamima
@ Jean-Luc Legras, I tried to run the script in linux, once it worked and generated all chromosome separately hapmap format file but I need one file including all chromosome.Another time did not, what can be done can you tell me?
Hi Shamima
In fact I had not seen you answer. Variscan works chromosome per chromosome, so that I have written the script this way. I think that it is easy then to collect each data file and combine them
Best.
JL
Hi Shamima
you can also use a program called NGSEP, it was made for SNPs identification but it does a lot of other stuff, like format converting. There´s a module to convert vcf files into several formats, for hapmap you may use java -jar NGSEPcore.jar ConvertVCF -printHapmap
I am a bit late to answer this. But somehow if your .vcf file size is huge you may find running Tassel-5-standalone on linux an easy tool to convert your huge .vcf file to hapmap file by using this short command line.
First bring the .vcf file i.e. “input” to the tassel directory
./run_pipeline.pl -Xmx5g -fork1 -vcf input -export -exportType Hapmap
The 5g argument here is for setting the space as per the size of your input file.
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