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Recent Votes
Comment: Problem to remove subset of patients with plink
Answer: scVelo on Seurat umap
Answer: Genbank vs SRA
H3K4Me3 ChIP-Seq signal at promoter
A: Use Tabix With A List Of Regions
Comment: Genbank vs SRA
Answer: Genbank vs SRA
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Recent Replies
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
No, in haplotypecaller
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
Then what is the best way to do slicing for 1Mb windows? Doing `--intervals` in the GenomicsDBImport?
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
> What is your suggestion to run GenomicsDBImport efficiently? call the GVCF by slices eg: chr1:1000000-2000000<br> run GenomicsDBImport …
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
I want to run gatk `GenomicsDBImport` tool to build a GenomicsDB. I want to slice it to reduce the computation time since I have 1300 gvcf …
Comment: Problem to remove subset of patients with plink
by
chrchang523
10k
The first step has to be taken outside of PLINK here. E.g. append "_1" and "_2" to the duplicated IDs in the .ped or .fam file, then menti…
Comment: Error in cnetplot enrichplot package
by
Ram
43k
Show us the exact call to `cnetplot()` with a sample of all input parameters. Did you compare notes with your friend?
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
why would you need to slice a gvcf file ? all the tools in gatk can use a BED / interval / chromosome to narrow the analysis
Comment: Error in cnetplot enrichplot package
by
Farhad
• 0
I check dataframe it has more than 2 columns
Comment: Error in cnetplot enrichplot package
by
Farhad
• 0
We write it to csv and then send it via email
Comment: Help with Base quality Score Recalibration (BQSR) using GATK
by
sainavyav22
• 0
Hi, Thanks for your reply. Are you aware of vcf file compatible to canfam 3.1 reference genome?
Comment: Error in cnetplot enrichplot package
by
Ram
43k
How does one "send" an in-memory data structure?
Answer: Help with Base quality Score Recalibration (BQSR) using GATK
by
Shred
★ 1.4k
Chromosome names from VCF and input files are not the same.
Comment: Should I use unpaired reads from trimmomatic
by
dxj294
• 0
I see, I have 186 paired and 93 unpaired. All the unpaired were from _2 fastq files. As of now I have started aligning only 186 paired, b…
Comment: Error in cnetplot enrichplot package
by
Farhad
• 0
See my friend sent me his data frame for me
Comment: Error in cnetplot enrichplot package
by
Ram
43k
That kind of context does not really help. Please show us: 1. "this analysis" - do you mean just the exact line of code above or is there …
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