LPA Server Pipeline

This repository includes the used pipeline for the article A comprehensive map of single base polymorphisms in the hypervariable LPA Kringle-IV-2 copy number variation region. The paper can be found here.

You can upload a BAM file and get annotated low-level variants in return. In the current version, indel detection and BAQ features are disabled.

BAM file creation

We recommend to use BWA-MEM to align your FASTQ files against a reference. Please use this reference for the alignment process.

bwa mem kiv2_6.fasta <file1.fastq> <file2.fastq>| gzip -3 > aln-pe.sam
samtools view -S -b aln-pe.sam > sample.bam

Data

All sequence data has been upload to Dataverse and can be accesed here.

Source Code

Please check out this repository if you want to have a look at the actual source code.

Pipeline Steps

• Low-level Variant Detection
• Type-B Base Annotation
• Region Annotation
• Overall Statistics

Run the LPA Pipeline

1. Install Cloudgene with the following commands

mkdir cloudgene
cd cloudgene
curl -s install.cloudgene.io | bash

2. Install the LPA workflow

./cloudgene gh seppinho/lpa-workflow

3a) Start the local web service and run

./cloudgene server

Open your web browser and enter http://localhost:8082. Use admin and admin1978 to login.

3b) Run on the command line

./cloudgene run seppinho-lpa-workflow --input <bam-folder> --archive <fasta file> --annotateBase <annotation file> --annotateRegion <region file>

Test Data

• Download BAM file

• Download Reference

• Download Base Annotation

• Download Region Annotation

./cloudgene run seppinho-lpa-workflow --input <bam-folder-withAK-Sample> --archive kiv2_6.fasta --annotateBase typeb_annotation.csv --annotateRegion maplocus_v3.txt

Download 1000G Paper Data

The script to download data from 1000 Genomes can be found here.

Contact

Please contact Stefan Coassin and Sebastian Schoenherr in case of problems.