WGS analysis

Runs with illumina human DNA-sequencing data. This goes through alignment, alignment quality control, data processing, variant calling, and variant filtration.

Piper is pipeline project started at the SNP&SEQ Technology platform built on top of GATK Queue. Piper WholeGenome is for human whole genome sequencing data. This goes through alignment, alignment quality control, data processing, variant calling, and variant filtration according to the best practice recommended by the Broad Institute, using primarily the GATK.

When we run analysis

We run this analysis by request for all WGS projects of human DNA where we have prepared the sequencing library in-house. If you have prepared a library yourself and we are just sequencing, please get in touch and mention that you would like us to run this analysis.

The analysis only works with human DNA (Homo sapiens, GRCh37 or GRCh38).

Please note that we can offer a specific analysis for tumor samples.

Input data

bcl2fastq demultiplexed FastQ files.

Results

The pipeline generates BAM alignment files and variant-calling VCF files.

Applications
Method Status

Service

We are routinely running this method. Please visit the Order Portal to place an order.

Keywords
Compatible Methods