@RudiC and @RavinderSingh13, thank you both for all of your help.
it looks like the script reads all the vcf files from REF and puts them in a variable FN. How do the txt files from VAL get used by the awk. The awk looks at each REF file and compares it to each VAL file looking for what's common and what's different. If a difference is found it identifies which file the missing data came from. The awk portion works on individual files, but I have over 500to compare so a loop would help, however that is what I need help with .
REF there are 250 files all located at /home/cmccabe/Desktop/comparison/reference/10bp
Code:
F13_ref_FP_10bp.txt
H19_ref_FP_10bp.txt
Data structure in REF
Code:
Chr Start End Ref Alt Func.refGene Gene.refGene Coverage Score A(#F,#R) C(#F,#R) G(#F,#R) T(#F,#R) Ins(#F,#R) Del(#F,#R) SNP Mutation Frequency Sanger
12 52200340 52200340 A C exonic SCN8A 4129 28.3 1560;1672 413;453 0;0 0;0 0;2 31;0 c.[5070A>C]+[=] 20.97
2 51254914 51254914 C T exonic NRXN1 1562 25.5 0;0 536;218 0;0 574;234 0;0 0;0 c.[498G>A]+[=] 51.73
X 67433722 67433722 C T exonic OPHN1 2747 25.6 0;0 46;37 0;0 1211;1443 1;8 5;5 c.[579G>A]+[579G>A] 96.61
VAL there are 250 files all located at /home/cmccabe/Desktop/comparison/validation/files
desired output (example not using these files that compares a REF file to a VAL file and finds what's in common, what's different, and where the difference comes from, it includes some additional data as well from another script)
Code:
Match:
Chr Start Ref Alt Func.refGene Gene.refGene Quality Reads Zygosity Phred
chr15 68521889 C T exonic CLN6 GOOD 50 het 4
chr7 147183143 A G intronic CNTNAP2 GOOD 382 het 22
chr2 167099158 A G exonic SCN9A GOOD 210 hom 55
Missing in Reference but found in IDP:
Chr Start Ref Alt Func.refGene Gene.refGene Quality Reads Zygosity Phred
chr2 51666313 T C intergenic NRXN1,NONE GOOD 108 het 7
chr2 166903445 T C exonic SCN1A GOOD 400 het 28
Missing in IDP but found in Reference:
Chr Start Ref Alt Func.refGene Gene.refGene Mutation Call Coverage Score Mutant Allele Frequency A(#F,#R) C(#F,#R) G(#F,#R) T(#F,#R) ins(#F,#R) del(#F,#R) SNP db_ref Region
2 166210776 C T exonic SCN2A c.[2994C>T]+[=] 3095 23.1 24.56 0:0 1158:1177 0;0 457;303 1;0 0;0 No low coverage
7 148106478 - GT intronic CNTNAP2 c.3716-5_3716-4insGT 4168 28.6 51.01 0;0 0;1 0;0 2199;1967 1129;997 0;1 rs60451214 No low
I hope this helps and apologize for the long post but think these are all the details. Thank you .
Last edited by cmccabe; 10-01-2016 at 10:49 AM..
Reason: added details
HI
I am trying to store the output of this awk command
awk -F, {(if NR==2) print $1} test.sr
in a variable when I am trying v= awk -F, {(if NR==2) print $1} test.sr
$v = awk -F, {(if NR==2) print $1} test.sr
but its not working out .
Any suggestions
Thanks
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10-01-2016
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