Vardict_paleisti

http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=678698205_C0Y8esueodF1NMKYgNEW3NyIUbUo&clade=mammal&org=Human&db=hg19&hgta_group=allTracks&hgta_track=knownGene&hgta_table=0&hgta_regionType=genome&position=chr21%3A33%2C031%2C597-33%2C041%2C570&hgta_outputType=primaryTable&hgta_outFileName=

#!/bin/bash
#
#for i in *.bam
#
#do
#
#echo "Indexing: "$i
#
#samtools index $i $i".bai"
#
#done

cd /home/farmacija/bin/vardict/VarDict-master
AF_THR="0.01" # minimum allele frequency
#./vardict -G ~/Downloads/hg19/hg19.fa -f $AF_THR -N test -b my.bam -c 1 -S 2 -E 3 -g 4 my.bed | ./teststrandbias.R | ./var2vcf_valid.pl -N test -E -f $AF_THR


#nohup sh -c "./vardict -G ~/Downloads/hg19/hg19.fa -f $AF_THR -N test -b /home/farmacija/HKMP-dysl/IonCode_0101_R_2018_04_19_05_33_53_user_S5-00727-7-cardio-dysl_Auto_user_S5-00727-7-cardio-dysl_140.bam -c 1 -S 2 -E 3 -g 4 /home/farmacija/Downloads/knownGene.bed | ./teststrandbias.R | ./var2vcf_valid.pl -N test -E -f $AF_THR" &

nohup sh -c "./vardict -G ~/Downloads/hg19/hg19.fa -f $AF_THR -N test -b /home/farmacija/HKMP-dysl/IonCode_0102_*.bam -c 1 -S 2 -E 3 -g 4 /home/farmacija/HKMP-dysl/kmp-dysl.bed | ./teststrandbias.R | ./var2vcf_valid.pl -N test -E -f $AF_THR" &