User: trausch
trausch • 1.2k
- Reputation:
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- Location:
- Germany
- Website:
- http://tobiasrausch.gi...
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- Joined:
- 3 years, 7 months ago
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Posts by trausch
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... We do have ab1 variant calling in Indigo [https://gear.embl.de/indigo/](https://gear.embl.de/indigo/) maybe that solves your problem? ...
written 4 days ago by
trausch • 1.2k
2
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5
answers
182
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5
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... I guess, he could just split and then cut away the first column.
bcftools query -f '%CHROM[\t%GT]\n' | awk '{print $0 >> "chrom"$1".bed"}'
...
written 8 weeks ago by
trausch • 1.2k
1
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5
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182
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... bcftools query should work.
bcftools query -H -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT]\n' ...
written 8 weeks ago by
trausch • 1.2k
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2
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201
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... Osx builds are skipped for performance reasons in the Bioconda versions, linux-64 is the default platform. You can either build from source on osx (requires boost library) or use [this minimal docker container of Alfred][1] (if you are familiar with docker).
[1]: https://hub.docker.com/r/trausch/ ...
written 9 weeks ago by
trausch • 1.2k
2
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2
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201
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2
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... [Alfred][1] can be used for that:
alfred count_dna -i exome.bed.gz -o coverage.gz input.bam
[1]: https://github.com/tobiasrausch/alfred ...
written 10 weeks ago by
trausch • 1.2k
1
vote
1
answer
283
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1
answers
... This should work using [Alfred][1]
./alfred consensus -f bam -t ont -p chr1:218992200
The alignment scoring depends on the sequencing technology. If you have phased SNPs and long reads you should split the BAMs into haplotypes prior to the consensus computation.
[1]: https://github.com/tob ...
written 3 months ago by
trausch • 1.2k
0
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2
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278
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... Thanks, did alfred work? ...
written 3 months ago by
trausch • 1.2k
0
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2
answers
278
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2
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... Another option is [Alfred][1]. We provide example quality control files for different sequencing assays (DNA-Seq whole-exome, ATAC-Seq, ...) and different sequencing technologies (Illumina, ONT, PacBio) at the [companion web application][2] so you can have a look if that's what you are looking for ( ...
written 3 months ago by
trausch • 1.2k
0
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2
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164
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... [Repli-Seq][1] can be used to map origins of replication. For humans there are likely cell-type-specific replication programs.
[1]: http://www.pnas.org/content/107/1/139 ...
written 3 months ago by
trausch • 1.2k
1
vote
1
answer
202
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1
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... [Delly][1] SV calls for the [HGSVC trios][2] are available [here][3].
[1]: https://github.com/dellytools/delly
[2]: https://www.biorxiv.org/content/early/2018/06/13/193144
[3]: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/hgsv_sv_discovery/working/20160930_pre_ashg_calls/2016100 ...
written 4 months ago by
trausch • 1.2k
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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7 months ago,
created 100 posts.
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For A: Methods of classifying, not detecting, structural variation?
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For A: Get trace data for all four bases from ab1 file
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12 months ago,
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: Methods of classifying, not detecting, structural variation?
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: Methods of classifying, not detecting, structural variation?
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3.0 years ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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