Filter out MC3 mutations that do not pass filter

website/data/mutations/annotate_mc3.sh

@@ -19,10 +19,11 @@ fi
 file=mc3.v0.2.8.PUBLIC.maf.gz   
 
 # get all columns required for annovar, skipping header line (first row)
-zcat $file | tail -n +2 | cut -f 5,6,7,11,47 > mc3.avinput
+# column 109 is filter
+zcat $file | tail -n +2 | awk '$109 == "PASS" {print $5,$6,$7,$11,$47,$16}' > mc3.avinput
 # reannotate all mutations on GRCh37/hg19
-./annovar/table_annovar.pl mc3.avinput humandb/ -buildver hg19 -out mc3_annotated -remove -protocol refGene -operation g -nastring . -thread 2
+./annovar/table_annovar.pl mc3.avinput humandb/ -buildver hg19 -out mc3_annotated -remove -protocol refGene -operation g -nastring . -thread 2 -otherinfo
 # add barcodes as comments; keep only those which are nonsynonymous SNVs
-paste <(cat mc3_annotated.hg19_multianno.txt) <(zcat $file  | cut -f 16) | awk -F '\t' '$9 ~ /nonsynonymous SNV/' | gzip > mc3_muts_annotated.txt.gz
+cat mc3_annotated.hg19_multianno.txt | awk -F '\t' '$9 ~ /nonsynonymous SNV/' | gzip > mc3_muts_annotated.txt.gz
 
 rm mc3.avinput