no indel calls

y4dary4dar TexasMember

Hi all,

I am using GATK to call SNPs and indels for eight mammal genomes with ~20X coverage and mapping to a reference genome.

I am able to get through the entire pipeline and call both SNPs and indels as directed in the tutorial -- mapping, sorting, RealignerTagetCreator, IndelRealigner, BaseRecalibrator, UnifiedGenotyper (due to processing issues, it will take about a month to run HaplotypeCaller), SelectVariants for SNPs, and SelectVariants for Indels.

I am able to identify plenty of SNPs using this method but my I am coming up empty with the indels. I get a vcf file with the proper headers but the list of indels is empty.

What should I look for to identify the problem? Any help would be appreciated.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Can you post an example IGV screenshot of an indel that should be called? Can you try running HaplotypeCaller on just one chromosome to check if any indels are called with it?


  • y4dary4dar TexasMember

    We are going in blind with these genomes and know of no specific indels we could test. Well, not exactly, we do know where there are some differential SINE insertions but it will take me a while to learn how to what you're asking.

    I will make an attempt at HaplotypeCaller using one of the larger contigs for the reference genome and get back to you.

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