rohit satyam
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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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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: gatk4-4.3.0.0-0b) Exact command used: gatk MarkDuplicatesSpark -I sample3_CNVP.sorted.bam -O sample3_CNVP.dedup.bam -M sample3_CNVP...
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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...
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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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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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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 ...