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Sequences Alignment and Sorting by Coordinate
(1)
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
Variant Annotation with VEP (Variant Effec...
(1)
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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