cre.gemini.get_variants4gene

README.md

@@ -172,6 +172,7 @@ vcf.platypus.getNV.sh ${family}-platypus-annotated-decomposed.vcf.gz
 * cre.coverage.bamstats05.sh - calculate coverage
 * cre.fixit.sh - fixes sample names
 * cre.gemini_load.sh loads vep-annotated vcf to gemini db.
+* cre.gemini.get_variants4gene.sh - pull all varaints for a specific gene.
 * cre.gnomad_scores.R - download and parse gnomad scores.
 * cre.immunopanels.R - annotates CRE report with 6 immunopanels.
 * cre.kinship.R - to plot relatedness (kinship) diagram for a group of samples. Sometimes helps to detect and solve mislabelling.

cre.bcbio.upgrade.star.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-#PBS -l walltime=23:00:00,nodes=1:ppn=10
+#PBS -l walltime=240:00:00,nodes=1:ppn=10
 #PBS -joe .
 #PBS -d .
 #PBS -l vmem=31g,mem=31g
@@ -10,9 +10,8 @@ which bcbio_nextgen.py
 hostname
 
 # sometimes cannot upgrade STAR on data nodes - memory is low, or cannot take much CPUs
+# can take more than a day
 export PATH=/hpf/largeprojects/ccmbio/naumenko/tools/bcbio_testing/bin:$PATH && STAR \
 --genomeDir /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_testing/genomes/Hsapiens/GRCh37/star \
 --genomeFastaFiles /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_testing/genomes/Hsapiens/GRCh37/seq/GRCh37.fa \
 --runThreadN 10 --limitGenomeGenerateRAM 30000000000 --genomeChrBinNbits 14 --runMode genomeGenerate --genomeSAindexNbases 14
-
-

cre.gemini.get_variants4gene.sh

@@ -1,3 +1,15 @@
 #!/bin/bash
+# use case:  when somebody wants to see all variants in a gene
+# usage: 
+# cre.gemini.get_variants4gene.sh [db] [sample] [gene]
+# output:
+# gene.csv
+
+db=$1
+sample=$2
+gene=$3
+
+query="select chrom,start+1 as pos,ref,alt,type,sub_type,gene,exon,codon_change,impact,gts."$sample",dp,rs_ids,gnomad_af_popmax,clinvar_sig,cadd_phred,hgvsc from variants where gene='"$gene"'"
+echo $query
+gemini query --header -q "$query" $db | sed s/"\t"/","/g > $gene.csv
 
-gemini query --header -q "select chrom,start+1,ref,alt,type,sub_type,gene,exon,codon_change,impact,gts.1247R_329260,depth,rs_ids,max_aaf_all,clinvar_sig,cadd_scaled,vep_hgvsc from variants where gene='NLRP3'" 1247R-ensemble.db > NLRP3.tsv