The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

empty vcf file after using VariantsToVCF

karin23karin23 Member Posts: 9
edited December 2013 in Ask the GATK team

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

Post edited by Geraldine_VdAuwera on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,421 admin

    Hi Karin,

    This probably indicates that the tool couldn't recognize the input format type. You may need to specify the format of your input variants file explicitly, e.g. if it's BED, you'd input it as --variant:BED mySNPs.bed.

    Geraldine Van der Auwera, PhD

  • karin23karin23 Member Posts: 9

    Hi Geraldine,

    thanks for the advive but, unfortunately, this does not help. I could also see before (when i didn't specify the file as a bed file), the following message: 'Dynamically determined type of mySNPs.bed to be BED, so it recognizes the file as a bed file.'

    Do you maybe have another idea?

    Thanks and sorry for bothering again,
    Karin

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,421 admin

    Hmm, either something is wrong with the file's formatting or something's buggy in the conversion. I'm running a few tests locally to check if the tool is behaving properly, I'll let you know what I find.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,421 admin

    Alright, it turns out the BED isn't actually a valid input for VariantsToVCF, even though it is listed as such in the docs. I'll try to sort out the inconsistency there, but in the meantime you'll need to generate your VCF some other way. Did your other SNP caller actually produce a BED file as output?

    Geraldine Van der Auwera, PhD

  • karin23karin23 Member Posts: 9

    Thanks Geraldine. No the SNP caller does not produce a BED file but a txt file with information on chr, pos, ref, alt, coverage ref, cov alt... and i converted it into bed because i thought VariantsToVCF works with bed.

    Bests, Karin

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,421 admin

    Ah, no you may be better off trying to load that text file directly. That sounds like the old dbsnp format, possibly.

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.