Extra_Features
Note: This section is for Advanced Users
The Core of vcfMerger2 is to merge 2 to N vcfs into one vcf without losing any data from all the vcfs. If this feature was the main driver for creating this tool, additional features have been implemented.
- preparing vcf for merging (
prep_vcf.sh) - making venn diagrams (
--do-venn) - filtering raw vcfs by PASS only when raw vcfs are the inputs of vcfMerger2.py (
--filter-by-pass). - filtering prepped vcfs before merging if variant-caller-specific filtering is needed before merging (
--filter)
Here a complete vcfMerger2 flowchart summary of the steps from raw vcfs to merged vcfs with filtering-prepped-filtering stages
for known variant caller, we provide scripts allowing preparing the tool-specific vcf to specifications for the merger tool
We provide a prep_vcf.sh script that allows to prep vcf independently from the main executable that is vcfMerger2.py located in the bin directory
Furthermore, we also provide a simplified way of filtering input vcf by PASS and to filter prepped vcfs the same way you would using snpSift directly.
Examples of different cases are available in the Examples section of the Wiki pages
[Advanced Users ; Under Development Features ]
if vcfMerger2 accepts RAW vcfs directly as inputs, this is because, in the background,
vcfMerger2 can modify internally the given raw vcfs and update them to vcfMerger2 specs before merging;
To do so, vcfMerger2 Team developed scripts as utilities that can also be used independently of vcfMerger2.py.
Scripts have been developed for the above listed variant callers.
If the variant caller is not listed above, users can make their own prep script for their tool then create a pull-request on github,
or open an issue with keyword improvement as first line in bloc text.
- To make somatic raw vcfs ready for vcfMerger2 merging step, the script
prep_vcf.shmay be used - To make germline raw vcfs ready for vcfMerger2 merging step, use
prep_vcf_germline.sh(feature under development)
These scripts can be found in the folders prep_vcfs and prep_vcfs_germline respectively
Usage Examples can be found in the Examples page;