User: trausch

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trausch760
Reputation:
760
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Trusted
Location:
Germany
Website:
http://tobiasrausch.gi...
Scholar ID:
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Last seen:
9 hours ago
Joined:
2 years, 5 months ago
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Posts by trausch

<prev • 82 results • page 1 of 9 • next >
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Comment: C: comparison of exome data to the 1000Genomes WGS data
... Thanks, so this is a population VCF with >10,000 samples? Then the callset is dominated by rare alleles such as singletons and doubletons of allele count 1 and 2. If you subset your VCF to common variants (MAF>1%) you will have a large intersection with 1000 Genomes and for the rare ones it is ...
written 5 days ago by trausch760
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Comment: A: comparison of exome data to the 1000Genomes WGS data
... 300,000 SNPs on chr1 for an exome capture data set? We usually have <100,000 confident exonic SNPs across the whole-genome for whole-exome sequencing. What is the on-target rate and the fraction of targets >=30x? ...
written 8 days ago by trausch760
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Comment: C: Unusual AF data (I think)
... Did you set missing genotypes to ref (-0) when using bcftools merge? ...
written 18 days ago by trausch760
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Answer: A: uniformity of coverage (pct > 0.2*mean) calculation/tool
... [htSeqTools][1] has a function to calculate the standardized SD of the genomic coverage. [Alfred][2] (disclaimer: our own tool) also calculates such a standardized SD of the genomic coverage. A pre-compiled static binary is available [here][3]. [1]: https://bioconductor.org/packages/release/bioc ...
written 7 weeks ago by trausch760
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Comment: C: ATACseq with STAR and macs2
... We use Bowtie for mapping, MACS for peak calling, IDR filtering of peaks and DESeq2 for differential peaks. Still work in progress but our current pipeline is on [github][1]. [1]: https://github.com/tobiasrausch/ATACseq ...
written 9 weeks ago by trausch760
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... It is a tab-delimited text file. You can use datamash to convert it to row-format: cat outprefix.metrics.tsv | datamash transpose | column -t The column-format is useful if you want to compare statistics across multiple samples because you can just concatenate the metrics files. ...
written 9 weeks ago by trausch760
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Answer: A: Calculating coverage for WGS, WES and RNASeq
... You can try [alfred][1] (disclaimer: our own tool). Example plots are here: [WGS][2] and [WES][3]. It also supports feature counting for RNA-Seq. [1]: https://github.com/tobiasrausch/alfred [2]: https://raw.githubusercontent.com/tobiasrausch/alfred/master/exampleplots/NA06985.pe.pdf [3]: ht ...
written 10 weeks ago by trausch760
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Answer: A: Explain the definition of DELLY output
... There is an online [Cancer Genomics Tutorial][1] available for Delly that explains many of these INFO fields. There is also a separate [Delly user group][2] that has some info about this. [1]: https://www.gitbook.com/book/tobiasrausch/tutorial-delly/details [2]: https://groups.google.com/forum ...
written 11 weeks ago by trausch760
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Answer: A: Any suggestion for sanger sequencing result editing
... We recently set up the web application [Indigo][1] that can analyze Sanger traces and aligns them to a reference genome or wildtype chromatogram. The [standalone command-line version][2] has a couple more features like dumping the whole Sanger trace as a tab delimited file so you can then indeed edi ...
written 11 weeks ago by trausch760
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Answer: A: Structural Variant annotation
... SVs are usually reported in VCF format. Such a VCF you can then annotate with [SnpEff][1], [VEP][2] or [Annovar][3]. Conversion to MAF for a tumor-normal VCF should be possible with [vcf2maf][4]. [1]: http://snpeff.sourceforge.net/ [2]: http://www.ensembl.org/info/docs/tools/vep/index.html [ ...
written 11 weeks ago by trausch760

Latest awards to trausch

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 3 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 4 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 4 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 4 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 9 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 21 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 22 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 22 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?

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