*** Test 3 : indexer vcf de reference
*** Test 3 sans filtre vep : idem
Benchmarking Summary:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al 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 276768 10535 266233 52169 10969 30616 3552 2122 0.038064 0.491069 0.586862 0.070652 NaN NaN 1.483361 0.509510
INDEL PASS 276768 10535 266233 52169 10969 30616 3552 2122 0.038064 0.491069 0.586862 0.070652 NaN NaN 1.483361 0.509510
SNP ALL 1937706 105753 1831953 357652 74634 177259 35111 797 0.054576 0.586270 0.495619 0.099857 2.0785 1.42954 1.539064 0.324923
SNP PASS 1937706 105753 1831953 357652 74634 177259 35111 797 0.054576 0.586270 0.495619 0.099857 2.0785 1.42954 1.539064 0.324923
*** Test 4 avec vcfeval sur vep_annot : idem
#+begin_src
#!/bin/bash
#SBATCH -c 4
#SBATCH -p smp
#SBATCH --time=01:00:00
#SBATCH --mem=32G
module load nix/2.11.0
export HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna dir=/Work/Groups/bisonex/data/NA12878/GRCh38
rtg vcfeval -b /Work/Groups/bisonex/data/NA12878/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -c files/vcf/NA12878_NIST7035_vep_annot.vcf.gz -o test-rtg -t /Work/Groups/bisonex/data/genome/GRCh38.p13/genomeRef.sdf
#+end_src
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
1.000 2984 2682 1840 3890296 0.5931 0.0008 0.0015
None 2984 2682 1841 3890296 0.5930 0.0008 0.0015
Exemple du log
2023-02-06 13:50:14 Reference NC_000001.11 baseline contains 307854 variants.
2023-02-06 13:50:14 Reference NC_000001.11 calls contains 426 variants.
2023-02-06 13:50:15 Reference NC_000002.12 baseline contains 325877 variants.
2023-02-06 13:50:15 Reference NC_000002.12 calls contains 320 variants.