Mercurial > repos > nick > allele_counts
comparison tests/artificial-nofilt.vcf.in @ 5:31361191d2d2
Uploaded tarball.
Version 1.1: Stranded output, slightly different handling of minor allele ties and 0 coverage sites, revised help text, added test datasets.
| author | nick |
|---|---|
| date | Thu, 12 Sep 2013 11:34:23 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 4:898eb3daab43 | 5:31361191d2d2 |
|---|---|
| 1 ##fileformat=VCFv4.1 | |
| 2 ##comment="ARGS=-H -r 1 -f 0 -c 0" | |
| 3 ##comment="This is a test set of made-up sites, each created in order to test certain functionality. It's meant to be run with -f 10 -c 10" | |
| 4 ##fileDate=19700101 | |
| 5 ##source=Dan | |
| 6 ##reference=file:///scratch/dan/galaxy/galaxy-central/database/files/002/dataset_0000.dat | |
| 7 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> | |
| 8 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> | |
| 9 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 10 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> | |
| 11 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> | |
| 12 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts"> | |
| 13 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT THYROID | |
| 14 # General note: the only data made consistent is the CHROM, POS, REF, ALT, and the variant data (after the ':'). The other stuff isn't supposed to be consistent. | |
| 15 # Simplest case, but POS 0 and no minor allele | |
| 16 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, | |
| 17 # Simple, normal cases of A/G variants: above/below threshold x strand bias/no strand bias (2 x 2 = 4 cases) | |
| 18 chr1 10 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,+G=1,-A=15,-G=1, | |
| 19 chr1 20 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,+G=1,-A=16, | |
| 20 chr1 30 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=10,+G=2,-A=11,-G=2, | |
| 21 chr1 40 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=11,+G=3,-A=11, | |
| 22 # Really low coverage | |
| 23 chr1 50 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=2,-A=1, | |
| 24 chr1 60 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=1,+G=1,-A=1,-G=1 | |
| 25 chr1 70 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=1,+G=1,-G=2, | |
| 26 chr1 80 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=102,+G=3,-A=2, | |
| 27 # Very low frequency tertiary allele | |
| 28 chr1 90 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=50,+G=5,+C=1,-A=50,-G=6,-C=1, | |
| 29 chr1 100 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=50,+G=5,-A=50,-G=6,-C=1, | |
| 30 # Only non-canonical alleles | |
| 31 chr1 120 . d1 . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=15,-d1=15, | |
| 32 # Same 4 cases, but with non-canonical major allele (d1) | |
| 33 chr1 130 . d1 G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=15,+G=1,-d1=15,-G=1, | |
| 34 chr1 140 . d1 G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=15,+G=1,-d1=16, | |
| 35 chr1 150 . d1 G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=10,+G=2,-d1=11,-G=2, | |
| 36 chr1 160 . d1 G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=11,+G=3,-d1=11, | |
| 37 # Test case where minor allele is above threshold on only one strand because of different coverage. Also, a long decimal minor allele frequency. | |
| 38 chr1 260 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=13,+G=7,-A=93,-G=7, | |
| 39 # Test case where minor alleles have equal frequency: Above/below threshold, +/- strand bias | |
| 40 chr1 300 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=1,+G=1,+T=38,-A=1,-G=1,-T=38, | |
| 41 chr1 310 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=6,+G=6,+T=38,-A=6,-G=6,-T=38, | |
| 42 chr1 320 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=6,+G=6,+T=38,-A=6,-G=6,-T=18, | |
| 43 chr1 330 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=6,+G=6,+T=38,-A=1,-G=1,-T=28, | |
| 44 chr1 340 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=1,+T=80,-G=1,-T=18, | |
| 45 chr1 350 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=11,+T=60,-G=11,-T=18, | |
| 46 # Case where + and - variants are interleaved with each other. Also, a long decimal result for the minor allele frequency. | |
| 47 chr1 400 . A N . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=16,-A=16,+G=4,-G=4, | |
| 48 # Test complex data in the ALT, INFO, and sample (before the ':') columns | |
| 49 chr1 410 . T G,A . . AC=1,1;AF=0.0111111111111,0.0111111111111 GT:AC:AF:NC 0/0:1,1:0.0111111111111,0.0111111111111:+A=1,+T=81,-T=16,-G=2, | |
| 50 chr1 420 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::+A=82,-A=22, |