Germline & Somatic short variant discovery (SNVs + Indels) for WGS & WES.
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  1. task ANNOVAR {
  2. File vcf
  3. String basename = basename(vcf,".vcf")
  4. String hg
  5. File annovar_database
  6. String docker
  7. String cluster_config
  8. String disk_size
  9. command <<<
  10. set -o pipefail
  11. set -e
  12. nt=$(nproc)
  13. if [ ${hg} == "hg38" ]; then
  14. /installations/annovar/table_annovar.pl ${vcf} ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
  15. fi
  16. if [ ${hg} == "hg19" ]; then
  17. /installations/annovar/table_annovar.pl ${vcf} ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,snp138,cosmic78,intervar_20170202,popfreq_all_20150413,clinvar_20190305 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
  18. fi
  19. >>>
  20. runtime {
  21. docker: docker
  22. cluster: cluster_config
  23. systemDisk: "cloud_ssd 40"
  24. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  25. }
  26. output {
  27. File avinput = "${basename}.avinput"
  28. File multianno_txt = "${basename}.${hg}_multianno.txt"
  29. File multianno_vcf = "${basename}.${hg}_multianno.vcf"
  30. }
  31. }