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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GetPileupSummaries error



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    Tanay Biswas
    Hi Genevieve

    Yes. It had the same issue. But I have solved it. Just one thing to ask that If I'm using WES data and I have the h19 covered (target) BED file which I lifted over to hg38, should I use -L covered.bed or -L gnomad.exomes.r2.sites.grc38.vcf while generating the pileups.table using ./gatk GetPileupSummaries ?

    Both the above files are now generating the output pileups.table but using -L covered.bed in the command reduces the pileups.table file size.

    Command 1:

    java -jar ~/gatk-package- GetPileupSummaries -I ~/TD2_fixmate_sorted_duprm.recal.bam -V /scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.gz -L /home/tbiswas/SureSelectV6_S07604514_hs_hg19/liftover_covered_hg38.bed -O /scratch/tbiswas/2/pileupsummeries/liftoverBED_TD_pileups.table (File size 1.8 MB)

    Command 2: 

    java -jar ~/gatk-package- GetPileupSummaries -I ~/TD2_fixmate_sorted_duprm.recal.bam -V /scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.gz -L /scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.gz -O /scratch/tbiswas/2/pileupsummeries/gatk43_P6-TD_pileups.table (File size 2.3 MB)

    Can you please elaborate on the fact and what sholud I do?


    Thank you.





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    Genevieve Brandt (she/her)

    Ok thank you, I am deleting the other post since it is a duplicate. We'll get back to you with a solution shortly!

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