Ashi
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Activity overview
Latest activity by Ashi-
Ashi created a post,
How do I add allele depth to Mutect2 output?
Tool version: GATK4.1.9.0 Sample: Whole genome sequence, human cancer. I need "allelic depth" (i.e, DepthPerAlleleBySample in Haplotypecaller)information in somatic.vcf for some further analysis....
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Ashi commented,
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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Ashi commented,
Hi, Thank you for clarification. Now, it works!!
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Ashi commented,
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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Ashi commented,
Thanks for update! Will change reference from hg19 to hg38.
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Ashi commented,
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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Ashi commented,
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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Ashi commented,
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...
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Ashi created a post,
How do I get known-SNP, Indel files in hg19 version?
I am trying to run BaseRecalibrator with my WGS data of human cancer samples according to current GATK best practice. My reference genome is hg19. To run BaseRecalibrator, I need known SNP, Indel...
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Ashi commented,
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:/...