Benchmarking Examples

High-confidence regions

• mergeBed.MajorityAlignersCallable.bed is obtained as described here. 

vcf-concat sSNV.MSDUKT.superSet.v1.2.vcf.gz sINDEL.MDKT.superSet.v1.2.vcf.gz \

| awk -F "\t" '$0 ~ /^#/ || $7 ~ /LowConf|Unclassified/' | vcfsorter.pl GRCh38.d1.vd1.dict - \

| egrep -v '^#' | awk -F '\t' '{print $1"\t"$2-11"\t"$2+10}' \

| bedtools subtract  -a mergeBed.MajorityAlignersCallable.bed -b stdin \

| bedtools intersect -a stdin -b genome.bed \

| bedtools subtract  -a stdin -b germline_chromosome_arm_loss.bed > High-Confidence_Regions_v1.2.bed

Example to benchmark a call set using hap.py software

docker run --rm -v /sc1:/sc1 -e HGREF=/sc1/PATH/GRCh38.d1.vd1.fa lethalfang/hap.py:latest \

/opt/hap.py/bin/som.py -N \

-o /sc1/PATH/hap.py/MuTect2_Results \

-r /sc1/PATH/GRCh38.d1.vd1.fa \

-R /sc1/PATH/High-Confidence_Regions_v1.2.bed \

/sc1/PATH/high-confidence_sSNV_in_HC_regions_v1.2.vcf.gz \

/sc1/PATH/WGS.bwa.dedup-IL_T_1_vs_IL_N_1-MuTect2.vcf.gz