Mercurial > repos > nick > allele_counts
diff tests/artificial-samples.vcf.in @ 5:31361191d2d2
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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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/artificial-samples.vcf.in Thu Sep 12 11:34:23 2013 -0400 @@ -0,0 +1,23 @@ +##fileformat=VCFv4.1 +##comment="ARGS=-f 10 -c 10" +##comment="This is a test set of made-up sites, in this case to test the handling of multiple read groups. It's meant to be run with -f 10 -c 10" +##fileDate=19700101 +##source=Dan +##reference=file:///scratch/dan/galaxy/galaxy-central/database/files/002/dataset_0000.dat +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> +##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BRAIN ARTERY THYROID +# naive case +chr1 0 . A G,C . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+G=15,-G=15, 0/0:1:1:+C=15,-C=15, +# cases all with one allele, but different minor allele numbers below threshold +chr1 10 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+A=15,+G=1,-A=15,-G=1, 0/0:1:1:+A=15,+G=1,-A=16, +# cases with different numbers of alleles +chr1 20 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,+G=1,-A=15,-G=1, 0/0:1:1:+A=17,+G=3,-A=17,-G=3, 0/0:1:1:+A=15,+G=2,-A=15, +# cases where some shouldn't be printed +chr1 30 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+A=9,-A=8, 0/0:1:1:+A=15,-A=9, +# cases with some complex pre-':' data +chr1 40 . T A,G,C . . AC=1,1;AF=0.0111111111111,0.0111111111111 GT:AC:AF:NC 0/0:1:1:+T=15,-T=15, 0/0:1,1:0.0111111111111,0.0111111111111:+A=1,+T=81,-T=16,-G=2, 0/0:3,1:0.0394736842105,0.0131578947368:+C=52,+T=30,-C=17,-T=1, \ No newline at end of file