******* HOLD Essai rtg tools
1. Générer SDf file
#+begin_src sh
rtg format genomeRef.fna -o genomeRef.sdf
#+end_src
Mais problème avec la comparaison
#+begin_src
$ rtg vcfeval -b dbSNP_common.vcf.gz -c clinvar.vcf.gz -o test -t genomeRef.sdf/^C
VCF header does not contain a FORMAT field named GQ
Error: Record did not contain enough samples: NC_000001.11 10001 rs1570391677 A,C . PASS RS=1570391677;dbSNPBuildID=154;SSR=0;PSEUDOGENEINFO=DDX11L1:100287102;VC=SNV;R5;GNO;FREQ=KOREAN:0.9891,0.0109,.|SGDP_PRJ:0,1,.|dbGaP_PopFreq:1,.,0;COMMON
#+end_src
******* DONE Essai bcftools
CLOSED: [2022-10-23 Sun 01:05]
#+begin_src sh
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -p common
#+end_src
On vérifie bien que les 2 fichiers commons on le même nombre de lignes
#+begin_src sh
$ grep -e '^NC' 0002.vcf | wc -l
74302
alex@gentoo ~/code/bisonex/data/common $ grep -e '^NC' 0003.vcf | wc -l
74302
#+end_src
******* DONE bedtools intersect
CLOSED: [2022-10-23 Sun 01:05]
#+begin_src sh
bedtools intersect -a dbSNP_common.vcf.gz -b clinvar.vcf.gz
#+end_src
$ wc -l intersect.vcf
220206 intersect.vcf