Merge pull request #105 from Rohan-cod/vcf-header

Update vcf files to include DP Format Header
elimuinformatics · Jun 8, 2022 · 6c1e229 · 6c1e229
2 parents 18501c9 + 0819207
commit 6c1e229
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diff --git a/vcf2fhir/test/vcf_example1.vcf b/vcf2fhir/test/vcf_example1.vcf
@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.1
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TEST001
 1	15	.	.	G	.	.	.	GT:PS	0/1:.
 1	16	.	A,T	G	.	.	.	GT:PS	0/1:.

diff --git a/vcf2fhir/test/vcf_example2.vcf b/vcf2fhir/test/vcf_example2.vcf
@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.1
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 10	96448001	.	T	<CGA_CNVWIN>	.	.	NS=1;CGA_WINEND=96450000	GT:CGA_GP:CGA_NP:CGA_CP:CGA_PS:CGA_CT:CGA_TS:CGA_CL:CGA_LS	.:0.87:0.92:2:53:=:53:0.999:707
 10	96448129	.	A	G	.	.	NS=1;AN=2;AC=1;CGA_XR=dbsnp.92|rs1926706;CGA_FI=1562|NM_000772.2|CYP2C18|INTRON|UNKNOWN-INC&1562|NM_001128925.1|CYP2C18|INTRON|UNKNOWN-INC;CGA_RPT=L1MA4A|L1|18.5	GT:PS:FT:GQ:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL:DP:AD:CGA_RDP	1/0:.:PASS:238:355,238:354,238:53,50:-355,0,-238:-53,0,-50:34:18,16:16

diff --git a/vcf2fhir/test/vcf_example4.vcf b/vcf2fhir/test/vcf_example4.vcf
@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.1
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample
 X	60466	.	T	C	.	.	NS=1	GT:PS:DP:AD:CGA_RDP	1|0:60454:48:17,31:31
 X	60579	.	G	A	.	.	NS=1	GT:PS:DP:AD:CGA_RDP	1|0:60579:47:24,23:23

diff --git a/vcf2fhir/test/vcftests.vcf b/vcf2fhir/test/vcftests.vcf
@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.1
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample
 X	60466	.	T	C	.	.	NS=1	GT:PS:DP:AD:CGA_RDP	1|0:60454:48:17,31:31
 X	60579	.	G	A	.	.	NS=1	GT:PS:DP:AD:CGA_RDP	1|0:60579:47:24,23:23