REQUIRED for all errors and issues:
a) GATK version used:gatk4-184.108.40.206-0
b) Exact command used:gatk GetPileupSummaries -I xx.bam -V somatic_hg38_af-only-gnomad.hg38.vcf.gz -L somatic_hg38_af-only-gnomad.hg38.vcf.gz -O pileups.table
c) Entire program log:Entire program log: Runs with no errors, but gets an empty result. And I did it in tumor-only mode. Only five lines of content are shown, which are contig，position，ref_count ，alt_count，other_alt_count ，allele_frequency. The reference genome was downloaded from the URL(https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0) and the somatic_hg38_af-only-gnomad.hg38.vcf.gz file was downloaded from the URL(https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38) . Is it an input error in my vcf.gz file? I would also like to ask if I need to mark duplicates when calling from the compared bam file, or do I just use the compared bam file? Can you tell me how to deal with it ? Thank you very much!
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