ASEReadCounter output wrong number of coverage

Question

[junhuili]

Hi,

I am using ASEReadCounter to count the number of reads per variant in a BAM file. For some positions, it will report 1 read covered(1 refCount or 1 altCount) while there is no read covered at those positions after checking it in bam files with IGVtools and samtools depth.

Is this a bug?

REQUIRED for all errors and issues:

a) GATK version used: 4.1.8.1

b) Exact command used:

java -Xms10g -XX:ParallelGCThreads=4 -jar gatk-package-4.1.8.1-local.jar ASEReadCounter -R hg19.chr.fa -I sample1.bam -V sample1.SNV.vcf -O sample1.ASE.tsv

Regards,

Junhui