Br User: Murilo Borges

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Name: Murilo Borges

Joined: Monday 27 April 2015 15:07:46 (UTC)

Last seen: Monday 27 June 2016 17:50:48 (UTC)

Email (public): murilogborges [at] hotmail.com

Website: Not specified

Location: Campinas, Brazil

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Field/Industry: Bioinformatics

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Workflow

Workflow Variant Annotation with VEP (Variant Effec... (1)

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Here, from a list of g.vcf files, we execute GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Created: 2016-05-16 | Last updated: 2016-07-06

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Workflow

Workflow Sequences Alignment and Sorting by Coordinate (1)

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We automatically retrieve BAM filenames based on the FASTA_R1 port name We assume FASTA_R1 name to be SAMPLENAME.R1.FASTQ or SAMPLENAME.R1.fastq.gz Alignment via Burrows-Wheeler transformation using BWA-MEM algorithm Sorts the input SAM or BAM Post Alignment File Processing We automatically retrieve BAM filenames based on the FASTA_R1 port name We assume FASTA_R1 name to be SAMPLENAME.R1.FASTQ or SAMPLENAME.R1.fastq.gz MarkDuplicates examines aligned records in the supplied SAM or BAM f...

Created: 2016-05-16 | Last updated: 2016-07-06

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