/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/expand.vcf is in r-bioc-variantannotation 1.20.2-1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | ##source=VariantTools 1.1.0
##phasing=unphased
##fileformat=VCFv4.1
##project=example
##fileDate=20121029
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AR,Number=A,Type=Integer,Description="ALT read counts">
##FORMAT=<ID=RR,Number=1,Type=Integer,Description="REF read count">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read count">
##FORMAT=<ID=AAP,Number=A,Type=Integer,Description="Flags indicating which ALTs are present">
##FORMAT=<ID=RAP,Number=1,Type=Integer,Description="Flag indicating if REF is present">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H1993
TP53 1000311 . T A . . DP=14;AF=0.5 AR:RR:DP:AAP:RAP 2:29:31:1:1
TP53 1011392 . C G . . . AR:RR:DP:AAP:RAP 540:41:582:1:1
TP53 1012027 . T C . . . AR:RR:DP:AAP:RAP 2:0:2:1:0
TP53 1012219 . G A . . . AR:RR:DP:AAP:RAP 2:0:2:1:0
TP53 1012654 . A G,T . . DP=10;AF=0.333,0.667 AR:RR:DP:AAP:RAP 585,4:1:590:2,2:1
TP53 1013309 . C G . . . AR:RR:DP:AAP:RAP 934:0:936:1:0
TP53 1017504 . A G . . . AR:RR:DP:AAP:RAP 2:3:5:1:1
TP53 1017549 . A G . . . AR:RR:DP:AAP:RAP 2:3:5:1:1
TP53 1019784 . T C . . . AR:RR:DP:AAP:RAP 5:0:5:1:0
TP53 1019934 . T C,A . . . AR:RR:DP:AAP:RAP 3,1:0:4:3,3:0
TP53 1019935 . G A . . . AR:RR:DP:AAP:RAP 3:0:3:1:0
TP53 1019986 . C T . . . AR:RR:DP:AAP:RAP 3:0:3:1:0
TP53 1020710 . A G . . . AR:RR:DP:AAP:RAP 3:1:4:1:1
TP53 1020776 . A G . . . AR:RR:DP:AAP:RAP 4:2:6:1:1
TP53 1020811 . A G . . . AR:RR:DP:AAP:RAP 2:4:6:1:1
TP53 1020837 . A G . . . AR:RR:DP:AAP:RAP 3:3:6:1:1
TP53 1020838 . A G . . . AR:RR:DP:AAP:RAP 2:4:6:1:1
TP53 1021339 . A G . . . AR:RR:DP:AAP:RAP 3:4:7:1:1
TP53 1021340 . A G . . . AR:RR:DP:AAP:RAP 3:4:7:1:1
TP53 1021638 . A G . . . AR:RR:DP:AAP:RAP 2:21:23:1:1
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