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Welcome to the ascatNgs wiki!

We will aim to provide both FAQ and guides for generating custom SNP profiles on this site.

!! This package is only suitable for WGS analysis, NOT WXS (exome/pulldown) !!

General

• Current protocols in Bioinformatics paper
  • Protocol Correction format of copynumber.caveman.csv
• Basic usage

Reference data

Please ensure that any reference files you use have the appropriate contig naming conventions. The GRCh37 examples here do not have a chr prefix. You can simply update the names appropriately.

Reference files for Human GRCh37 can be found here.

For Human GRCh38 the relevant reference file can be obtained as described here

There are a couple of methods available to generate the relevant SNP loci.

Generating reference files from public VCF datasets

The pages listed here are tried and tested methods of generating SnpGcCorrections.tsv files from public datasets. Generally these include helper scripts or commands known to work with the file format at time of creation.

• Human reference files from 1000 genomes VCFs
• Mouse reference files using Mouse Genome Project VCF files

Generating reference files from BWA-mem mapped normal BAM/CRAM files

The following page describes a generic way to create a custom SnpGcCorrections.tsv from your own normal sample data.

• Reference files from normal sample data

Generating species specific gender loci file

If you wish the program to do automatic gender detection then specify gender loci file to option -locus
Create a species and build specific gender loci file in following format [ e.g., GRCh37d5_Y.loci]

Y       4546684
Y       2934912
Y       4550107
Y       4549638