GATK_pipeline

• GATK 4.1.8 version
• Call somatic short variants and generate a bamout with Mutect2

Processing Steps

1. Lift genome positions

UCSC provides binary liftOver tools to convert BED file from one genome assembly to another.

NOTE: Use the 'chr' before each chromosome name

2. BedToIntervalList (Picard)

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

Running pipeline

The script for pipeline run_gatk.sh Submit a Job: An example is available here

Annotation

liftover VCF from hg38 to hg19 & ANNOVAR

The script for ANNOVAR run_annotation.sh Submit a Job: An example is available here

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Reference Links

• LiftOver

• Mutect2

• BedToIntervalList (Picard)