# Tagged with #variantstovcf 1 documentation article | 0 announcements | 8 forum discussions

A new tool has been released!

Check out the documentation at VariantsToVCF.

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Hi there can any body help me in knowing how we can calculate or find frequency of a heterozygous carrier from the Allele frequency in vcf file Regards

I’d like to convert a hapmap file to vcf. The hapmap file is from http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/latest/forward/non-redundant/genotypes_chr1_ASW_r27_nr.b36_fwd.txt.gz

java -Xmx2g -jar GenomeAnalysisTK.jar \
-R ref.fasta \
-T VariantsToVCF \
-o output.vcf \
--variant:RawHapMap input.hapmap \
--dbsnp dbsnp.vcf

1. Since the hapmap is in reference genome b36, should the ref.fasta be b36 as well? While b37 is everywhere, the only place I can find b36 is b36.3 at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/build36.3/Homo_sapiens_NCBI_build36.3.tar.gz, is this OK?
2. What’s the usage of “-–dbsnp” here, should it be dbSNP built upon b36 as well?

Thanks,

Hi,

I have annotated my vcf file of 20 samples from Unified genotyper using the following steps.

Unified genotyper->Variantrecalibration->Applyrecalibration->VariantAnnotator

My question is how should I proceed if I have to select rare variants (MAF<1%) for the candidate genes that I have,for each of these 20 samples?

Hi,

i have SNPs from another SNP caller which does not produce vcf files so i wanted to convert those using the VariantsToVCF walker. I used the following command:

java -Xmx2g -jar  /PATH/TO/GenomeAnalysisTK.jar -T VariantsToVCF -R reference.fa -o mySNPs.vcf --variant mySNPs.bed


GATK version 2.7-4

i took a bed file as input which had the following format:

chr1    895 896
chr1    941 942
chr1    1096    1097
...


The walker runs without any error message but i get an empty vcf file (0B, nothing) apart from a mySNPs.vcf.idx and a mySNPs.bed.idx file.

Any idea how to fix that?

Thanks a lot!!!

Best wishes, Karin