Mercurial > repos > nick > allele_counts

annotate tests/artificial-samples.vcf.in @ 11:cf2af5c3118c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/dunovo commit ac9577f0047ad984b307fe2c4b40e2eb45a0e6e2"
author nick
date Fri, 03 Apr 2020 16:05:04 -0400
parents 31361191d2d2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
1 ##fileformat=VCFv4.1
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
2 ##comment="ARGS=-f 10 -c 10"
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
3 ##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"
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
4 ##fileDate=19700101
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
5 ##source=Dan
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
6 ##reference=file:///scratch/dan/galaxy/galaxy-central/database/files/002/dataset_0000.dat
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
7 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
8 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
9 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
10 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
11 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
12 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
13 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BRAIN ARTERY THYROID
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
14 # naive case
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
15 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,
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
16 # cases all with one allele, but different minor allele numbers below threshold
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
17 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,
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
18 # cases with different numbers of alleles
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
19 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,
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
20 # cases where some shouldn't be printed
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
21 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,
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
22 # cases with some complex pre-':' data
31361191d2d2 Uploaded tarball.
nick
parents:
diff changeset
23 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,