Ashi
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Hi, I am trying to run BaseRecalibrator with my WGS data. My ref is hg19 reference. Where can I get SNP and Indel vcf files in hg19 version? I found b37 version files (below) in google cloud gs:/...
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Hi I have another question about hg38 genome reference fasta file. I downloaded "Homo_sapiens_assembly38.fasta" from your Google Cloud bucket https://console.cloud.google.com/storage/browser/genomi...
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Hi, Thank you for clarification. Now, it works!!
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I have same error using GATK4.1.9.0 docker in HPC. I did not understand previous comments completely. Please let me make it sure. My reference directory has:hg38.fasta with index, dic fileshg38_v0_...
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Thanks for update! Will change reference from hg19 to hg38.
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Hi, I have an another question. For GetPileupSummaries step, can I specify normal.bam files separately like this?: gatk GetPileupSummaries \ -I normal1.bam \ -I normal2.bam \ -I normal3.bam...
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Hi, My sample is WGS FFPE (tumor matched with normal tissue). I would like to add "Read Orientation Artifacts Workflow" to this workflow. How do I do it? Could you please add some hands-on script i...
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I could not understand this new pipeline of Mutect2 (4.1.1.0, or newer). My samples are tumor with matched normal tissue, WGS. Ref is hg38. Tissue type is FFPE. Could anyone tell me how to call som...