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Losing info fields using bcftools merge

vcf merge bcftools gnomad written 7 weeks ago by dayne.filer • 0

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157

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Fill a VCF record field that is partially annotated

vcf vcfanno gnomad snp written 3 months ago by joangibert14 • 0 • updated 3 months ago by Pierre Lindenbaum ♦ 112k

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1.1k

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How to extract gnomad exomes bgz

bgz gnomad written 4 months ago by stanedav • 20 • updated 4 months ago by Pierre Lindenbaum ♦ 112k

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699

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Difference in allele count between ExAC and gnomad exomes

exome exac gnomad written 6 months ago by dolevrahat • 10 • updated 6 months ago by Kevin Blighe ♦ 28k

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396

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gnomAD variant frequencies by study

tcga gnomad exac written 6 months ago by igor ♦ 6.6k

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1.3k

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News: The genome Aggregation Database (gnomAD)

news gnomad written 19 months ago by Pierre Lindenbaum ♦ 112k

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621

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genotype frequency data

frequency genotype gnomad written 22 months ago by aidpranculis • 0 • updated 22 months ago by Ron • 810

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Recent Replies

C: GSEA results change in clusterProfiler by sugus • 20
Actually nothing happened when I set logical seed. The results still change.
C: Did anyone manage to successfully run HLAScan and get results? by ngs_star • 0
Hi. This is very basic question but I am trying to run HLAscan and getting error. $ ./hla_sc...
C: Seeking ideas and guidance for an undergraduate project by steve • 1.7k
You can replicate some of the aspects of the study here: https://genomemedicine.biomedcentral.com...
C: Efficient way to convert several lists into a present/absent binary format? by Kevin Blighe ♦ 28k
Do you mean that the genes have to match on the same row?
C: gene expression analysis using RNA seq data by Kevin Blighe ♦ 28k
If you just take HTseq counts, then these are 'raw' counts and are not normalised. You may mean n...
C: RNA-Seq DEGenes Without GTF by Kevin Blighe ♦ 28k
Valeu, cara!
C: what read should i use for classifying? by life99945 • 0
Thank you for the answer! I'v got this extended file from laboratory along with forward and reve...
C: Very low mapping rate of mRNA seq data by Mehmet • 410
Addition to suggestions by ATpoint, you can check several contamination: 1. Bacteria or virus u...
C: what read should i use for classifying? by h.mon ♦ 19k
I've never used it, so I can't vouch for the results claimed in the paper, but in principle [IM-T...
C: Very low mapping rate of mRNA seq data by Seq225 • 50
Thank you. The reads are good quality (almost all of them). Not sure about any sort of contamin...
C: How to combine two .sam files? by ATpoint ♦ 7.5k
Your command is wrong. Samtools works like this: ## Option 1: use -o to write the output to ...
C: Very low mapping rate of mRNA seq data by ATpoint ♦ 7.5k
Did you consider to have poor-quality data? Could be contaminated with genomic DNA, or contaminat...

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