From 7a1398c02fca07f9b5f7e5af21d111a28aa180df Mon Sep 17 00:00:00 2001 From: "naumenko.sa" Date: Fri, 24 Aug 2018 14:45:59 -0400 Subject: [PATCH] bug fix --- cram2fq.sh | 2 +- cre.gemini2txt.vcf2db.sh | 6 +++--- cre.vep.sh | 35 +++++------------------------------ 3 files changed, 9 insertions(+), 34 deletions(-) diff --git a/cram2fq.sh b/cram2fq.sh index a973d3b..391cc48 100755 --- a/cram2fq.sh +++ b/cram2fq.sh @@ -22,4 +22,4 @@ cramtools fastq -Xmx10g -F $sample --skip-md5-check \ -R /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa mv $sample_1.fastq.gz $sample_1.fq.gz -mv $sample_2.fastq.gz $sample_2.fq.gz \ No newline at end of file +mv $sample_2.fastq.gz $sample_2.fq.gz diff --git a/cre.gemini2txt.vcf2db.sh b/cre.gemini2txt.vcf2db.sh index 6e3ff85..f3552d9 100755 --- a/cre.gemini2txt.vcf2db.sh +++ b/cre.gemini2txt.vcf2db.sh @@ -56,9 +56,9 @@ sQuery="select \ start+1 as Pos,\ aa_change as AA_change,\ hgvsc as Codon_change,\ - af_esp_aa as Evs_af_aa,\ - af_esp_ea as Evs_af_ea,\ - af_esp_all as Evs_af_all,\ + af_evs_aa as Evs_af_aa,\ + af_evs_ea as Evs_af_ea,\ + af_evs as Evs_af_all,\ phylop20way_mammalian as Conserved_in_20_mammals, gts," diff --git a/cre.vep.sh b/cre.vep.sh index 9166aa8..81ac906 100755 --- a/cre.vep.sh +++ b/cre.vep.sh @@ -1,9 +1,9 @@ #/bin/bash -# gemini.vcf2vep - annotate vcf with vep before loading to gemini database +# gemini.vcf2vep annotates vcf with vep before loading to gemini database # based on bcbio.log -# uses hgvs notation and no --pick - all effects for a gene -# 10h is not enough for genomes or big multisample vcfs +# uses hgvs notation and no --pick = all effects for a gene +# 10h walltime is not enough for genomes or big multisample vcfs #PBS -l walltime=23:00:00,nodes=1:ppn=1 #PBS -joe . @@ -17,32 +17,7 @@ fi bname=`basename $vcf .vcf.gz` -# old one for VEP87 -#unset PERL5LIB && export PATH=/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin:$PATH && /home/naumenko/work/tools/bcbio/anaconda/bin/variant_effect_predictor.pl --vcf -o stdout \ -# -i $vcf --species homo_sapiens --no_stats --cache --offline --dir /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/vep --symbol --numbers --biotype --total_length \ -# --canonical --gene_phenotype --ccds --fields Consequence,Codons,Amino_acids,Gene,SYMBOL,Feature,EXON,PolyPhen,SIFT,Protein_position,BIOTYPE,CANONICAL,CCDS,HGVSc,HGVSp \ -# --plugin LoF,human_ancestor_fa:/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/variation/human_ancestor.fa.gz --sift b --polyphen b --hgvs --shift_hgvs 1 \ -# --fasta /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa \ -# | sed '/^#/! s/;;/;/g' | bgzip -c > $bname.vepeffects.vcf.gz - -# old one for VEP88 -#unset PERL5LIB && export PATH=/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin:$PATH && /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin/vep \ -# --vcf -o stdout -i $vcf --fork 7 --species homo_sapiens --no_stats --cache --offline --dir /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/vep \ -# --symbol --numbers --biotype --total_length --canonical --gene_phenotype --ccds --uniprot --domains --regulatory --protein --tsl --appris --af --max_af --af_1kg --af_esp \ -# --af_exac --pubmed --variant_class --fasta /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa.gz \ -# --plugin LoF,human_ancestor_fa:/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/variation/human_ancestor.fa.gz --sift b --polyphen b --hgvs --shift_hgvs 1 --merged \ -# | sed '/^#/! s/;;/;/g' | bgzip -c > $bname.vepeffects.vcf.gz - -#old one for VEP90 -#unset PERL5LIB && export PATH=/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin:$PATH && /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin/vep --vcf -o stdout \ -# -i $vcf --fork 5 --species homo_sapiens --no_stats --cache --offline --dir /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/vep --symbol --numbers --biotype --total_length \ -# --canonical --gene_phenotype --ccds --uniprot --domains --regulatory --protein --tsl --appris --af --max_af --af_1kg --af_esp --af_gnomad --pubmed --variant_class \ -# --fasta /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa.gz \ -# --plugin LoF,human_ancestor_fa:/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/variation/human_ancestor.fa.gz \ -# --plugin MaxEntScan,/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/share/maxentscan-0_2004.04.21-0 --plugin SpliceRegion --sift b --polyphen b --hgvs --shift_hgvs 1 --merged \ -# | sed '/^#/! s/;;/;/g' | bgzip -c > $bname.vepeffects.vcf.gz - -#the old one +#VEP91.2 #unset PERL5LIB && export PATH=/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin:$PATH && /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin/vep --vcf -o stdout \ # -i $vcf --fork 5 --species homo_sapiens --no_stats --cache --offline --dir /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/vep --symbol --numbers --biotype --total_length \ # --canonical --gene_phenotype --ccds --uniprot --domains --regulatory --protein --tsl --appris --af --max_af --af_1kg --af_esp --af_gnomad --pubmed --variant_class \ @@ -68,4 +43,4 @@ unset PERL5LIB && vep --vcf -o stdout \ --plugin SpliceRegion --sift b --polyphen b --hgvs --shift_hgvs 1 --merged \ | sed '/^#/! s/;;/;/g' | bgzip -c > $bname.vepeffects.vcf.gz -tabix $bname.vepeffects.vcf.gz +tabix $bname.vepeffects.vcf.gz \ No newline at end of file