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License: MIT License
Code for the aldosterone-producing adenoma sequencing project
License: MIT License
The pipeline still needs CNV calling.
The script should perform CNV calling an all input BAM files.
It should allow:
Possible tools to integrate:
The "--CREATE_INDEX" seems to not work in GatherVcfs. Repalce with tabix if necessary.
Restructure the alignment and calling folders into own Repos and just use commands to execute those in this project.
Write README updates for all analyses performed and commands executed.
Write documentation on methods used and software versions used.
The script should calculate typical NGS QC measurements and should ideally be applicable to both FASTQ and BAM files.
Tools to use:
Ideally it generate reports per input and a sumamry report over all analyses (R script).
For some samples there is a problem in "gatk_calculate_contamination.smk" that causes the script to break. It seems to be related to not enought disk sapce somehow. Maybe a temp dir problem.
Stats files are currently named "_merged" while the VCF files are not. This genrates a problem in downstream analyses where the stats file is not automatically found.
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