diff test-data/sniper_results.vcf @ 0:70999d19997f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sniper_results.vcf	Mon Jul 02 11:16:55 2018 -0400
@@ -0,0 +1,20 @@
+##fileformat=VCFv4.1
+##fileDate=20180622
+##phasing=none
+##reference=file:///export/gatkhg38pl/GRCh38.d1.vd1.fa
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
+##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
+##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
+##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
+##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
+##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
+##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
+chr22	22714396	.	G	A	.	.	.	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:15:0,15,0,0:0,0,15,0:72:.:0:30:60:60:0:.	0/1:0/1:41:0,28,0,13:13,0,28,0:59:.:59:30,31:60:60,60:2:45
+chr22	22714411	.	T	C	.	.	.	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:9:0,9,0,0:0,0,0,9:54:.:0:30:60:60:0:.	0/1:0/1:28:0,22,0,6:0,6,0,22:32:.:32:32,31:60:60,60:2:27