cleaning up src directory and updating head.html

[arvados-tutorial.git] / src / annotation / runcommand

diff --git a/src/annotation/new/runcommand b/src/annotation/runcommand
similarity index 61%
rename from src/annotation/new/runcommand
rename to src/annotation/runcommand
index 4fad7656451c9d5816b61f64edf35248def869b3..fd2e78407f468ed0e35f5f0600f13eef04ae3516 100644 (file)
--- a/src/annotation/new/runcommand
+++ b/src/annotation/runcommand
@@ -4,4 +4,8 @@ bcftools annotate -a /data-sdd/keep/by_id/80aadf801bccd1e1d838b07d46d4de63+1712/
 bcftools filter -i "INFO/ALLELEID!=[]" annotated.vcf | bcftools query -f'%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n' > reportdata.txt
 # converting data to correct format and to JSON output for report generation
 # for link: https://www.ncbi.nlm.nih.gov/clinvar/variation/128475/
+
+# putting above together
+bcftools annotate -a /data-sdd/keep/by_id/80aadf801bccd1e1d838b07d46d4de63+1712/37/clinvar.vcf.gz -c ID,INFO /data-sdd/keep/by_id/542f0989c5ee117e20d293ef82311192+114145/hu34D5B9_var-GS000015891-ASM.vcf.gz | bcftools filter -i "INFO/ALLELEID!=[]" | bcftools query -f'%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n' > reportdata.txt
+
 python generatereport.py