zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

fixing the tests; Bamboo captured the failure in the logs correctly. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3610 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-06-22 18:38:03 +00:00
parent a6d3e4bd47
commit 18f62a346d
2 changed files with 22 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
testdata/vcfExmaple.vcf4 → testdata/vcf/vcfWithGenotypes.vcf vendored
View File

@ -21,4 +21,5 @@
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 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
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
20 1234587 supersite GGGG G 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/0:17:2 1/1:40:3
20 1234587 supersite GGGG G 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/0:17:2 1/1:40:3
22 17580633 . ACNCCTAANCC AC 100 PASS NS=3;DP=9;AA=G GT:GQ:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.

20
testdata/vcf/vcfWithoutGenotypes.vcf vendored 100644
View File

@ -0,0 +1,20 @@
##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">
#CHROM POS ID REF ALT QUAL FILTER INFO
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ
20 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G
20 1234587 supersite GGGG G 50 PASS NS=3;DP=9;AA=G