Imported Upstream version 0.7

[pysam.git] / tests / example.vcf40

diff --git a/tests/example.vcf40 b/tests/example.vcf40
new file mode 100644 (file)
index 0000000..07e0746
--- /dev/null
+++ b/tests/example.vcf40
@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##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 NA00002 NA00003
+M      1230237 .       T       .       47      PASS    NS=3;DP=13;AA=T GT:GQ:DP:HQ     0|0:54:7:56,60  0|0:48:4:51,51  0/0:61:2
+17     14370   rs6054257       G       A       29      PASS    NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ     0|0:48:1:51,51  1|0:48:8:51,51  1/1:43:5:.,.
+20     17330   .       T       A       3       q10     NS=3;DP=11;AF=0.017     GT:GQ:DP:HQ     0|0:49:3:58,50  0|1:3:5:65,3    0/0:41:3
+20     1110696 rs6040355       A       G,T     67      PASS    NS=2;DP=10;AF=0.333,0.667;AA=T;DB       GT:GQ:DP:HQ     1|2:21:6:23,27  2|1:2:0:18,2    2/2:35:4
+20     1234567 microsat1       GTCT    G,GTACT 50      PASS    NS=3;DP=9;AA=G  GT:GQ:DP        0/1:35:4        0/2:17:2        1/1:40:3