If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 188.8.131.52
b) Exact command used:
gatk GetPileupSummaries -I ../SRR10022835.md.bam -V $breast/chr17.af-only-gnomad.raw.sites.hg19.vcf.gz -L $breast/chr17.af-only-gnomad.raw.sites.hg19.vcf.gz -O SRR10022835.test.pileups.table
c) Entire error log:
If not an error, choose a category for your question(REQUIRED):
c) Why do I see (......)?
Why when I run GetPileupSummaries on bam file that has duplicates marked with gnomadVCF are all columns ref_count, alt_count, other_alt_count zeros for all rows even when there is an alignment at the position? This is WXS. I also aligned reads with bowtie2 will defaults.
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