Empty output of allele specific expression analysis by GATK

Question

[zizigolu]

Hi,

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?

[WouterDeCoster]

It may be obvious, but you used the same reference for your WGS and RNA-seq, right? Same chromosome names...

[zizigolu]

Actually I am being given .BAM both for RNA-seq and WGS but I guess they used the same genome from name of BAM files

HUMAN_1000Genomes_hs37d5_RNA_seq_121_1pre.dupmarked.bam

And I have used the same for gatk ASE

[Phoenix Mu]

Did you make sure that your sample names in VCF file can be found as Read group in BAM file?