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Specify more than one snpmask with Fasta Alternate Reference Maker

Hi there,

I am hoping to use multiple snpmask vcfs with fasta alternate reference maker. The description of fasta alternate reference maker says "...it allows for one or more "snpmask" VCFs to set overlapping bases to 'N'."

However, I haven't been able to figure out how to specify multiple snpmasks.

I have tried

--snpmask mask1.vcf mask2.vcf 


--snpmask mask1.vcf --snpmask mask2.vcf

but both give the error:

Argument 'snpmask' has too many values.

Both mask1.vcf and mask2.vcf work fine on their own (when only one snpmask specified).

I am using GATK v3.8-0.

My apologies for this very basic question! I've read the documentation carefully and searched for "--snpmask" in the forums, but am still stuck - any pointers would be appreciated!



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @elguevaraI think it's the first time anyone has asked for this, as far as I can recall from doing this for 6 years :)

    Since this is an older version, a lot of people are out on vacation, and the original author of the tool left a long time ago, it might be difficult to get you a timely answer to your actual question. However, in the interest of getting you through this, I would recommend creating a combined VCF out of your two VCFs just for the purpose of masking. You should be able to use CombineVariants with default settings.

    Good luck!

  • elguevaraelguevara Member

    Thank you for the reply, Geraldine.

    Part of the reason I posted the question was actually because I ran into trouble with CombineVariants. Ultimately I found a workaround, but to make a long story short, I had three vcf files containing different kinds of low quality variants that I wanted to use as snpmasks for FARM. I produced these vcfs using SelectVariants and the outside program SnpSift. Specifically, I used SelectVariants to produce two vcfs - one each of low quality indels and low quality snps, while I used SnpSift to pull out all variants with a GQ < 30. I can use CombineVariants to combine the two vcfs produced by SelectVariants, but when I try to combine them with the SnpSift produced vcf, I get an error saying that CombineVariants shouldn't be used on gvcfs, even though my files are not gvfs.

    Fortunately, I was able to get around this by using VCFtools vcf-merge and then using the resulting combined vcf as a snpmask.

    I just wanted to post this in case anyone else runs into this issue. It seems like using multiple snpmasks in FARM isn't strictly necessary given these available options for combining vcfs, but it might save someone some time one day (maybe in another 6 years!) if the documentation for FARM was changed to say that it allows for one snpmask vcf rather than "one or more" :)

    Thanks again for the support, as well as the great tools.


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