rohit satyam
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Activity overview
Latest activity by rohit satyam-
rohit satyam created a post,
Should we run MarkDuplicates on PCR-Free Libraries made using PCR-Free Kits to take care of Optical Duplicates ?
I found a post here that states we shouldn't run MarkDuplicates on the data produced using PCR-Free Kits. So should we use it to mark optical duplicates because Illumina platform generates a lot of...
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rohit satyam commented,
Hi Genevieve Brandt (she/her). Thanks for your input. We suspected something to be fishy with the demultiplexing step and it turns out to be true. We got it demultiplexed it again and now it works ...
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rohit satyam commented,
Hi Genevieve Brandt (she/her) My BWA command ran successfully on 9 pairs of the data without any error. The new preprocessing pipeline of GATK as mentioned here and the one you mentioned should pr...
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rohit satyam created a post,
SAMException: Value was put into PairInfoMap error even after using -M flag
Hi Everyone. I am facing a nontrivial issue at the markduplicates step in all the 14 pairs (samples of cancer). I keep on getting PairInfoMap error in all of my samples because of some unknown reas...
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rohit satyam commented,
Hi, is there any update on the proper documentation of the Mitochondrial Variant Analysis. I am really finding it difficult to understand really what sequence of steps must be followed for finding ...
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rohit satyam commented,
Hi Sir I have currently 23 Tumor vs Normal samples. According to GATK Best Practices, it is desirable if not necessary to include PONS as described here and here. My question is would PONS using 23...
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rohit satyam commented,
Wow. Thanks a lot. David Benjamin
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rohit satyam created a post,
Which file is af-only-gnomad.hg38.vcf.gz?
AnsweredHi Team!! I have been searching for a file named : af-only-gnomad.hg38.vcf.gz I went to gnomad website and downloaded the file All chromosomes VCF (.tbi) from the gnomADv3 tab. The file is overw...
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rohit satyam commented,
Hi David Benjamin Thanks for your prompt response. How about calling variants using different tools like DeepVariants, Mutect2, and Varscan and then intersecting the VCF files to rule out false pos...
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rohit satyam created a post,
How to compensate for absence of normals for few samples?
Dear Team I currently have 50 cancer samples (breast cancer). However, for 15 samples, I don't have adjacent normals. I wish to call somatic mutations. I know for 15 samples I can call variants in ...