Changes to calling and merging somatic variants

[skchronicles]

No description provided.

[skchronicles]

Results: Sample HG002

Benchmarking command:

ml singularity
singularity run \
     --bind $PWD,/data/NCBR/references/wgs_truthset,/data/NHLBI_IDSS/dev/tmp,/data/OpenOmics/references \
     hap.py_latest.sif \
         /opt/hap.py/bin/hap.py \
             --threads 12 \
             -o $PWD \
             -r /data/OpenOmics/references/genome-seek/Homo_sapiens_assembly38.fasta \
             -f /data/NCBR/references/wgs_truthset/benchmark/HG002_GRCh38_1_22_v4.1_draft_benchmark.bed \
            /data/NCBR/references/wgs_truthset/benchmark/HG002_GRCh38_1_22_v4.1_draft_benchmark.vcf.gz \
            ${outdir}/deepvariant/VCFs/HG002.germline.vcf.gz

Benchmarking summary of germline variants from hap.py:

Type	Filter	TRUTH.TOTAL	TRUTH.TP	TRUTH.FN	QUERY.TOTAL	QUERY.FP	QUERY.UNK	FP.gt	METRIC.Recall	METRIC.Precision	METRIC.Frac_NA	METRIC.F1_Score	TRUTH.TOTAL.TiTv_ratio	QUERY.TOTAL.TiTv_ratio	TRUTH.TOTAL.het_hom_ratio	QUERY.TOTAL.het_hom_ratio
INDEL	ALL	526124	522121	4003	883050	1240	359667	236	0.992392	0.997631	0.407301	0.995004			1.5282123912	1.66704493722
INDEL	PASS	526124	522097	4027	881395	1226	358049	236	0.992346	0.997657	0.40623	0.994995			1.5282123912	1.66242418643
SNP	ALL	3365379	3344115	21264	3794070	3891	443806	1207	0.993682	0.998839	0.116974	0.996253	2.09971069792	1.99949184864	1.58097758955	1.53108490286
SNP	PASS	3365379	3344106	21273	3794005	3891	443745	1207	0.993679	0.998839	0.11696	0.996252	2.09971069792	1.99953529946	1.58097758955	1.53104151662