- GATK 4.1.8 version
- Call somatic short variants and generate a bamout with Mutect2
UCSC provides binary liftOver tools to convert BED file from one genome assembly to another.
NOTE: Use the 'chr' before each chromosome name
Converts from BED to the Picard interval_list format. This tool requires a sequence dictionary, provided with the SEQUENCE_DICTIONARY or SD argument.
liftoverbed_IntervalList.sh
The script for pipeline run_gatk.sh
Submit a Job: An example is available here
liftover VCF from hg38 to hg19 & ANNOVAR
The script for ANNOVAR run_annotation.sh
Submit a Job: An example is available here