29Aug2014

1. Get a list of vcf hts file (snp.raw.snpFingerPrintingTest.vcf)

ODIN: LIstOfVcfOdin.txt

find /Volumes/data1.odin/001_exome/diagnosticSamples/ -type f -name "*snp.raw.snpFingerPrintingTest.vcf"| grep 060_delivery >LIstOfVcfOdin.txt  

LOKI: LIstOfVcfLoki.txt

find /data/diag/samples/ -type f -name "*snp.raw.snpFingerPrintingTest.vcf"| grep 060_delivery >~/LIstOfVcfLoki.txt

2. Get the values for each snps on each files:

   j=0;for i in cat LIstOfVcfOdin.txt ;do echo $i $((j++));echo -e $i"\t\t\t\t\t\t\t\t\t" >$j.csv ;python GenotypeFingerPrinting.py $i >> $j.csv ;done

check for files with number of lines difference then 26 ( correct number )

wc -l *csv|sort  
 1 6.csv
 1 98.csv
 1 99.csv
26 1.csv
 .
 .
 26 96.csv
 26 97.csv  

remove files

6.csv: /Volumes/data1.odin/001_exome/diagnosticSamples//PCD/Sample_Diag-excap19-13000161501-PCD-KIT-Av5.140103_7001448_0252_BC3F4UACXX/060_delivery/Sample_Diag-excap19-13000161501-PCD-KIT-Av5.140103_7001448_0252_BC3F4UACXX.snp.raw.snpFingerPrintingTest.vcf

98.csv: /Volumes/data1.odin/001_exome/diagnosticSamples//LMBB/Sample_Diag-excap19-13000852600-LMBB-KIT-Av5.140103_7001448_0251_AC3831ACXX/060_delivery/Sample_Diag-excap19-13000852600-LMBB-KIT-Av5.140103_7001448_0252_BC3F4UACXX.snp.raw.snpFingerPrintingTest.vcf

99.csv: /Volumes/data1.odin/001_exome/diagnosticSamples//LMBB/Sample_Diag-excap19-13000709802-LMBB-KIT-Av5.140103_7001448_0252_BC3F4UACXX/060_delivery/Sample_Diag-excap19-13000709802-LMBB-KIT-Av5.140103_7001448_0252_BC3F4UACXX.snp.raw.snpFingerPrintingTest.vcf

mv 6.csv 6
mv 98.csv 98
mv 99.csv 99

concatanet all the files into one

paste *csv >all.csv;open all.csv

in excel choose data to columns option then save the file as a xlsx file.

####Do the Same in Loki:

j=0;for i in ` cat LIstOfVcfLoki.txt` ;do echo $i $((j++));echo -e $i"\t\t\t\t\t\t\t\t\t" >$j.csv ;python GenotypeFingerPrinting.py $i >> $j.csv  ;done

wc -l *csv|sort
1 7.csv
26 10.csv  

remove the faulty file (7.csv)
7.csv: /data/diag/samples/EE/Sample_Diag-excap25-14000334301-EE-KIT-Av5.140603_SN586_0192_AC446MACXX/060_delivery/Sample_Diag-excap25-14000334301-EE-KIT-Av5.140603_SN586_0192_AC446MACXX.snp.raw.snpFingerPrintingTest.vcf

mv 7.csv 7

paste *csv >all.csv

Find which snp was faulty