ASEReadCounter output wrong number of coverage

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JUNHUI LI

• December 01, 2023 15:00

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

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  Ricky Magner

  • December 08, 2023 20:59

  Hi,

  Do you think you can provide an example for debugging purposes, of one line from the VCF and one line from the BAM file that contribute in an unexpected manner towards the count from ASEReadCounter that you found when looking in IGV?

  Thanks,

  Ricky

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