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fixed dbNSFPAnnotation tool (some obscure first line pushed in by dbNSFP will be removed if it exists) #258

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merged 2 commits into from
Aug 7, 2015
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fixed dbNSFPAnnotation tool (some obscure first line pushed in by dbNSFP will be removed if it exists) #258

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63052d3
fixed dbNSFPAnnotation tool (some obscure first line pushed in by dbN…
RoanKanninga Aug 5, 2015
85934ef
increased memory size for BwaAlign
RoanKanninga Aug 5, 2015
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2 changes: 1 addition & 1 deletion compute5/NGS_DNA-3.0.1/protocols/BwaAlign.sh
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Original file line number Diff line number Diff line change
@@ -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
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43 changes: 28 additions & 15 deletions compute5/NGS_DNA-3.0.1/protocols/dbNSFPAnnotation.sh
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Expand Up @@ -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),
Expand Down Expand Up @@ -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