diff --git a/compute5/NGS_DNA-3.0.1/protocols/BwaAlign.sh b/compute5/NGS_DNA-3.0.1/protocols/BwaAlign.sh index f47b1067..bddcc4e3 100755 --- a/compute5/NGS_DNA-3.0.1/protocols/BwaAlign.sh +++ b/compute5/NGS_DNA-3.0.1/protocols/BwaAlign.sh @@ -1,4 +1,4 @@ -#MOLGENIS walltime=20:00:00 nodes=1 ppn=8 mem=8gb +#MOLGENIS walltime=20:00:00 nodes=1 ppn=8 mem=10gb #Parameter mapping #string stage diff --git a/compute5/NGS_DNA-3.0.1/protocols/dbNSFPAnnotation.sh b/compute5/NGS_DNA-3.0.1/protocols/dbNSFPAnnotation.sh index 81ba7974..8a93d4a0 100755 --- a/compute5/NGS_DNA-3.0.1/protocols/dbNSFPAnnotation.sh +++ b/compute5/NGS_DNA-3.0.1/protocols/dbNSFPAnnotation.sh @@ -16,21 +16,25 @@ #optional annotation columns ###Build 37 --> dbnsfp 2.7 -#chr,pos(1-coor),ref,alt,aaref,aaalt,hg18_pos(1-coor),genename,Uniprot_acc,Uniprot_id,Uniprot_aapos, -#Interpro_domain,cds_strand,refcodon,SLR_test_statistic,codonpos,fold-degenerate,Ancestral_allele, -#Ensembl_geneid,Ensembl_transcriptid,aapos,aapos_SIFT,aapos_FATHMM,SIFT_score,SIFT_converted_rankscore, -#SIFT_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score, -#Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,LRT_score,LRT_converted_rankscore,LRT_pred, -#MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,MutationAssessor_score, +#chr,pos(1-coor),ref,alt,aaref,aaalt,rs_dbSNP141,hg18_pos(1-coor),hg38_chr,hg38_pos, +#genename,Uniprot_acc,Uniprot_id,Uniprot_aapos,Interpro_domain,cds_strand,refcodon, +#SLR_test_statistic,codonpos,fold-degenerate,Ancestral_allele,Ensembl_geneid,Ensembl_transcriptid, +#aapos,aapos_SIFT,aapos_FATHMM,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Polyphen2_HDIV_score, +#Polyphen2_HDIV_rankscore,Polyphen2_HDIV_prePolyphen2_HVAR_score,Polyphen2_HVAR_rankscore, +#Polyphen2_HVAR_pred,LRT_score,LRT_converted_rankscore,LRT_pred,MutationTaster_score, +#MutationTaster_converted_rankscore,MutationTaster_pred,MutationAssessor_score, #MutationAssessor_rankscore,MutationAssessor_pred,FATHMM_score,FATHMM_rankscore,FATHMM_pred, -#RadialSVM_score,RadialSVM_rankscore,RadialSVM_pred,LR_score,LR_rankscore,LR_pred,Reliability_index, -#CADD_raw,CADD_raw_rankscore,CADD_phred,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP46way_primate, -#phyloP46way_primate_rankscore,phyloP46way_placental,phyloP46way_placental_rankscore, -#phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phastCons46way_primate,phastCons46way_primate_rankscore, +#RadialSVM_score,RadialSVM_rankscore,RadialSVM_pred,LR_score,LR_rankscore,LR_pred, +#Reliability_index,VEST3_score,VEST3_rankscore,CADD_raw,CADD_raw_rankscore,CADD_phred, +#GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP46way_primate,phyloP46way_primate_rankscore, +#phyloP46way_placental,phyloP46way_placental_rankscore,phyloP100way_vertebrate, +#phyloP100way_vertebrate_rankscore,phastCons46way_primate,phastCons46way_primate_rankscore, #phastCons46way_placental,phastCons46way_placental_rankscore,phastCons100way_vertebrate, -#phastCons100way_vertebrate_rankscore,SiPhy_29way_pi,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,LRT_Omega, -#UniSNP_ids,1000Gp1_AC,1000Gp1_AF,1000Gp1_AFR_AC,1000Gp1_AFR_AF,1000Gp1_EUR_AC,1000Gp1_EUR_AF,1000Gp1_AMR_AC, -#1000Gp1_AMR_AF,1000Gp1_ASN_AC,1000Gp1_ASN_AF,ESP6500_AA_AF,ESP6500_EA_AF +#phastCons100way_vertebrate_rankscore,SiPhy_29way_pi,SiPhy_29way_logOdds, +#SiPhy_29way_logOdds_rankscore,LRT_Omega,UniSNP_ids,1000Gp1_AC,1000Gp1_AF,1000Gp1_AFR_AC, +#1000Gp1_AFR_AF,1000Gp1_EUR_AC,1000Gp1_EUR_AF,1000Gp1_AMR_AC,1000Gp1_AMR_AF,1000Gp1_ASN_AC, +#1000Gp1_ASN_AF,ESP6500_AA_AF,ESP6500_EA_AF ,ARIC5606_AA_AC,ARIC5606_AA_AF,ARIC5606_EA_AC, +#ARIC5606_EA_AF,clinvar_rs,clinvar_clnsig,clinvar_trait #### Build 38 --> dbnsfp v3 and higher #### ##chr,pos(1-based),ref,alt,aaref,aaalt,rs_dbSNP142,hg19_chr,hg19_pos(1-based),hg18_chr,hg18_pos(1-based), @@ -88,7 +92,16 @@ dbnsfp \ -f Ensembl_geneid,GERP++_RS,Polyphen2_HDIV_pred,Polyphen2_HVAR_pred,SIFT_score,CADD_raw,CADD_raw_rankscore,CADD_phred,FATHMM_score,SiPhy_29way_logOdds,phastCons100way_vertebrate,1000Gp1_EUR_AF,ESP6500_EA_AF \ ${variantAnnotatorSampleOutputSnpsFilteredVcf} > ${tmpDbNSFPSampleVcf} -mv ${tmpDbNSFPSampleVcf} ${dbNSFPSampleVcf} -echo "mv ${tmpDbNSFPSampleVcf} ${dbNSFPSampleVcf}" +FIRSTLINE=`head -1 ${tmpDbNSFPSampleVcf}` + +if [[ $FIRSTLINE == *"hg38"* ]] +then + sed '1d' ${tmpDbNSFPSampleVcf} > ${dbNSFPSampleVcf} + echo "removed first line of ${tmpDbNSFPSampleVcf} and moved file to ${dbNSFPSampleVcf}" +else + mv ${tmpDbNSFPSampleVcf} ${dbNSFPSampleVcf} + echo "mv ${tmpDbNSFPSampleVcf} ${dbNSFPSampleVcf}" + +fi