diff test-data/output.g.vcf @ 2:98fe794d2ec0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 4255237ed7a51299e25bd7de7ad52ac5d419a56c
author iuc
date Sun, 04 Sep 2022 07:54:30 +0000
parents 7608209110d3
children 918c8b94c8d8
line wrap: on
line diff
--- a/test-data/output.g.vcf	Fri Oct 01 07:46:42 2021 +0000
+++ b/test-data/output.g.vcf	Sun Sep 04 07:54:30 2022 +0000
@@ -12,7 +12,7 @@
 ##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
 ##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
-##DeepVariant_version=1.2.0
+##DeepVariant_version=1.4.0
 ##contig=<ID=K03455,length=9719>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR8525881
 K03455	1	.	T	<*>	0	.	END=1000	GT:GQ:MIN_DP:PL	0/0:1:0:0,0,0
@@ -20,12 +20,12 @@
 K03455	2001	.	T	<*>	0	.	END=2597	GT:GQ:MIN_DP:PL	0/0:1:0:0,0,0
 K03455	2598	.	G	<*>	0	.	END=2598	GT:GQ:MIN_DP:PL	./.:0:2:59,6,0
 K03455	2599	.	A	<*>	0	.	END=2603	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
-K03455	2604	.	CCA	C,<*>	5.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:5:2:0,2,0:1,0:3,15,0,990,990,990
+K03455	2604	.	CCA	C,<*>	7.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:7:2:0,2,0:1,0:6,16,0,990,990,990
 K03455	2607	.	A	<*>	0	.	END=2607	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
-K03455	2608	.	A	T,<*>	7.8	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:7:2:0,2,0:1,0:6,14,0,990,990,990
-K03455	2609	.	A	T,<*>	4.8	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:4:2:0,2,0:1,0:2,14,0,990,990,990
+K03455	2608	.	A	T,<*>	7.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:7:2:0,2,0:1,0:6,15,0,990,990,990
+K03455	2609	.	A	T,<*>	6.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:6:2:0,2,0:1,0:5,17,0,990,990,990
 K03455	2610	.	G	<*>	0	.	END=2612	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
-K03455	2613	.	A	T,<*>	1.1	RefCall	.	GT:GQ:DP:AD:VAF:PL	./.:7:2:0,2,0:1,0:0,19,5,990,990,990
+K03455	2613	.	A	T,<*>	3.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:3:2:0,2,0:1,0:0,8,0,990,990,990
 K03455	2614	.	A	<*>	0	.	END=2614	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
 K03455	2615	.	A	<*>	0	.	END=2615	GT:GQ:MIN_DP:PL	0/0:15:5:0,15,149
 K03455	2616	.	C	<*>	0	.	END=2616	GT:GQ:MIN_DP:PL	./.:0:7:8,0,158
@@ -34,10 +34,10 @@
 K03455	2619	.	T	<*>	0	.	END=2619	GT:GQ:MIN_DP:PL	0/0:21:7:0,21,209
 K03455	2620	.	G	<*>	0	.	END=2620	GT:GQ:MIN_DP:PL	0/0:39:13:0,39,389
 K03455	2621	.	G	<*>	0	.	END=2651	GT:GQ:MIN_DP:PL	0/0:50:49:0,147,1469
-K03455	2652	.	G	A,<*>	20.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:20:201:0,201,0:1,0:20,47,0,990,990,990
+K03455	2652	.	G	A,<*>	23.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:23:201:0,201,0:1,0:23,36,0,990,990,990
 K03455	2653	.	T	<*>	0	.	END=2659	GT:GQ:MIN_DP:PL	0/0:50:201:0,300,2999
-K03455	2660	.	T	C,<*>	25.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:25:213:0,213,0:1,0:25,45,0,990,990,990
+K03455	2660	.	T	C,<*>	21.9	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:213:0,213,0:1,0:21,30,0,990,990,990
 K03455	2661	.	T	<*>	0	.	END=2663	GT:GQ:MIN_DP:PL	0/0:50:213:0,300,2999
-K03455	2664	.	A	G,<*>	21.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:238:0,238,0:1,0:21,45,0,990,990,990
+K03455	2664	.	A	G,<*>	21.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:238:0,238,0:1,0:21,33,0,990,990,990
 K03455	2665	.	C	<*>	0	.	END=2668	GT:GQ:MIN_DP:PL	0/0:50:240:0,300,2999
-K03455	2669	.	G	A,<*>	20.6	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:250:0,250,0:1,0:20,42,0,990,990,990
+K03455	2669	.	G	A,<*>	15.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:16:250:0,250,0:1,0:15,32,0,990,990,990