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I am not able to find ReadCountWalker function by googing

I want to quantify expressed SNV from mutations called from RNA-seq and SNV called from WGS. I head about ReadCountWalker function but I am not able to find anything about that by googling; Any help please?

Thanks a lot


  • fi1d18fi1d18 Member

    I need help please

    I have a RNA-seq .BAM file for each patient. Also, for each patient I have done whole genome sequencing and I have .BAM files. By strelka I called mutations and I got .vcf. Now, when I used .BAM file of RNA-seq and .vcf file from WGS for allele specific expression analysis by gatk, I got an empty file

    This is the command I used

    gatk ASEReadCounter \
    -R hs37d5.fa \
    -I RNA-seq.bam \
    -V WGS.vcf.gz \
    -O output.table

    Can any of you done allele specific expression analysis help me to see where I am doing wrong? Should I first call mutation on RNA-seq .BAM files and use that instead of WGS?

    Any comments please about where potentially I could go wrong?
  • bshifawbshifaw Member, Broadie, Moderator admin
    edited July 2019

    GATK can be sensitive with the input files that you provide, outputs generated from other tools could cause some issues. Try validating your BAM and VCF files

    Also there is a caveat with this tool mentioned in the tool doc

    This tool will only process biallelic het SNP sites. If your callset contains multiallelic sites, they will be ignored. Optionally, you can subset your callset to just biallelic variants using e.g. SelectVariants with the option "-restrictAllelesTo BIALLELIC".

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