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position indel, variant calling

I am implementing my pipeline for Roche 454 and I have used GATK for called of variants.
I have compared my variants with Roche's variants and for BRCA1 my variants corresponded, but the position of indel for BRCA2 are wrong, the vcf file reported that them position is a few bp before (instead the positions of snp are right)
I have searched on genome browser and I have seen that the positions of Roche were right.

For example, this are the coordinates that I have in my files.
32893207 32893197 T/-
32900342 32900337 A/-
32900370 32900363 T/-
32900376 32900371 C/-
32900933 32900933 T/A
32907208 32907202 A/-
32907428 32907420 A/-
32907546 32907535 TTT/-

Could help me?

Best Answer


  • SteveLSteveL BarcelonaMember

    This may depend on the surrounding sequence - the variant co-ordinate reported by GATK may be left-aligned.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    Can you post some example VCF records? Also, LeftAlignAndTrimVariants may be useful in your case.


  • The problem is that for Roche I do not have a vcf, I have a file that includes variants with them start/end position.
    So I do not use LeftAlignAndTrimVariants with this files. Anyway thank you

  • marktongmarktong USAMember
    edited March 2016

    I do not agree with Steve on which t was deleted. It matters in term that HGVS recommends the one on most 3' end are changed. This means, a simple left alignment tool is not enough when we generating HGVS compliant variant names.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @marktong This question of what is the correct way to represent variants is a complicated and largely unsolved problem, which we address by using clearly defined conventions. GATK uses the left-alignment convention, but of course if what you need is right-alignment, or some other convention, then you will need to find some utility that provides the necessary conversion. At this time GATK does not offer that functionality.

  • marktongmarktong USAMember
    edited March 2016

    Thanks for Geraldine for response to my comments. I understand variant naming is complicated. But I believe if GATK can provide a right alignment tool, that will largely solve the strand specific alignment requirement (only + and - strand). I understand left-align is conventional, but it does not help providing a correct alignment in generating HGVS compliant variant names.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    I don't think there will be any plans for making a right alignment tool in the near future, as we stick to the left convention.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @marktong Please understand that our development is driven primarily by the needs of our in-house analysis pipelines, and we typically don't have the resources to add features on request. We do try to be responsive to the needs of the scientific community of course, and on occasion we have been able to devote resources to developing specific features that were in particularly high demand (such as non-diploid organism support). But to be frank it's the first time someone has requested this as far as I can remember. If others write in to tell us this is a big need, we'll consider adding it. For now however I'm afraid we can't do anything for you.

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