I have file (VCF) as like this
##fileformat=VCFv4.0
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001
Chr02 259 . A . 20 . . GT:DP:A:C:G:T:PP:GQ 0/0:1:0,1:0,0:0,0:0,0:0,26,23,75,33,33,33,47,52,49:23
Chr02 260 . C . 13 . . GT:DP:A:C:G:T:PP:GQ 0/0:1:0,0:0,1:0,0:0,0:24,0,70,17,25,49,43,25,25,44:16
Chr02 261 . C . 13 . . GT:DP:A:C:G:T:PP:GQ 0/0:1:0,0:0,1:0,0:0,0:24,0,194,18,25,49,44,25,25,45:16
Chr02 262 . C A 21 . . GT:DP:A:C:G:T:PP:GQ 0/1:1:0,0:0,1:0,0:0,0:387,0,342,348,25,368,376,25,25,368:25
Chr02 263 . C . 24 . . GT:DP:A:C:G:T:PP:GQ 0/0:2:0,0:1,1:0,0:0,0:541,0,529,495,29,556,508,29,29,499:29
Chr02 264 . A . 31 . . GT:DP:A:C:G:T:PP:GQ 0/0:2:1,1:0,0:0,0:0,0:0,280,192,317,36,36,36,178,302,219:36
Chr02 265 . G C 25 . . GT:DP:A:C:G:T:PP:GQ 0/1:2:0,0:0,0:1,1:0,0:255,414,0,328,284,29,284,29,351,29:29
Chr02 266 . A . 31 . . GT:DP:A:C:G:T:PP:GQ 0/0:2:1,1:0,0:0,0:0,0:0,281,323,440,36,36,36,209,309,315:36
Chr02 267 . C . 24 . . GT:DP:A:C:G:T:PP:GQ 0/0:2:0,0:1,1:0,0:0,0:595,0,541,481,28,567,512,28,28,512:
I need to split this file based on the number of lines(1000) and count "0/1" from each file(splitted file). For this purpose I splitted the files using this command
head -10 Chromosome02.vcf| tee header subset.1.VCF >/dev/null ; awk -v header="`cat header`" -v count=1 '( (NR>10) && !( (NR-1) % 2) ) { count++ ; print header >"subset." count ".VCF";} {print $0 >>"subset." count ".VCF";}' Chromosome02.vcf | grep “0/1”
But it is not working. Is there any way to do this without generating the split files ?
Expected output
Chromosome02
00
00
01
00
01
00
tail -n +11 file |
awk -v n=1000 '/0\/1/{c++} NR%n==0{print c; c=0} END {if (NR%n!=0) print c}'
The tail command will exclude the headers from the file. Then we count the lines containing the pattern, but every N lines we print and reset the counter.