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ASEReadCounter contruct a heterozygous VCF input file for all nucleotides in region of interest

mdjohnson30mdjohnson30 CambridgeMember

The aim is to identify any and all bi-allelic SNPs in my region of interest.
Then determine if there is allelic imbalance in all my RNA-seq samples.

I already filtered the BAM files for the region of interest and managed to produce a vcf file for the matching region.

However the documentation for the ASEReadCounter states that the input:
"A VCF file with specific sites to process."

Is it possible to construct a vcf file (of my region of interest) where I have bi-allelic information for every single base? How can this be done since there would be 3 different alternative alleles? Would this actually work in ASEReadCounter?

I'm trying to avoid making a vcf file for each sample and using the same vcf file as input for ASEReadCounter. Do I have the right understanding? In other words, where does the original vcf input file come from?

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @mdjohnson30
    Hi,

    To get just the biallelic sites, you can use SelectVariants with --restrictAllelesTo BIALLELIC.

    However, I think you should be fine inputting the VCF straight from HaplotypeCaller, as I think ASEReadCounter ignores sites that are not biallelic.

    You can use the multi-sample VCF for all of your samples. The tool will match the sample name in the BAM file to the sample name in the VCF :smile:

    -Sheila

  • nbartoniceknbartonicek AustraliaMember

    Thank you for the active support regarding your tools!

    Is there a sample workflow, or a tutorial on how to establish allelic imbalance of RNAseq data with ASEReadCounter? I used GATK tools to produce the bam files and the according vcf files through HaplotypeCaller.

    Any help appreciated!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    You're welcome! Unfortunately we don't have any detailed materials on ASEReadCounter beyond the tool doc. That being said the usage example in the tool doc is the standard command you would use to invoke it for that purpose.
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