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PostsRecent activity by rohit satyam Sort by recent activity
MarkDuplicatesSpark only supports singleton fragments and pairs. We found the following group with >2 primary reads
REQUIRED for all errors and issues: a) GATK version used: gatk4-22.214.171.124-0b) Exact command used: gatk MarkDuplicatesSpark -I sample3_CNVP.sorted.bam -O sample3_CNVP.dedup.bam -M sample3_CNVP...
Using gatk VariantFiltration to filter ONT wf-artic generated VCF files
Will it be valid to use gatk VariantFiltration on the variant calls generated using wf-artic pipeline? I am asking this because we have both Illumina and ONT runs for few samples and we wish to che...
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...
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...
Which file is af-only-gnomad.hg38.vcf.gz?Answered
Hi 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...
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 ...