Question about the allele depth generated by haplotypecaller and ASEReadCounter

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杨烁

• March 27, 2023 09:00

I've got a problem while using HaplotypeCaller and ASEReadCounter, as I could not obtain the same allele depth in the output vcf file and table file.

The cmd I applied is as following:

gatk --java-options "-Xmx32g" HaplotypeCaller -R hg38.fa -I sample.markdup.chr22.bam -O sample.chr22.g.vcf.gz -ERC GVCF

gatk --java-options "-Xmx32g" GenotypeGVCFs -R hg38.fa -V sample.chr22.g.vcf.
gz -O sample.all.chr22.vcf.gz

gatk --java-options "-Xmx32g" ASEReadCounter -R hg38.fa -I sample.markdup.chr22.bam -V sample.all.chr22.onlySNP.vcf.gz -O sample.all.final.table
--min-mapping-quality 20 --min-depth-of-non-filtered-base 8 --min-base-quality 18 > ASEReadCounter.log 2>&1

 

should I add any additional parameters to ASEReadCounter?

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  James Emery

  • March 29, 2023 18:51

  Hello. ASEReadCounter is an old tool part of our original RNA pipeline and it is not currently part of our RNA best practices so this tool should be considered use at your own risk. We do not have a set of recommendations for how best to run it under the conditions you have listed here. 

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