TAB delimited output format (tsv) for variants about exomiser

[damiansm]

Sure but we prob want to spec what goes in it though. If we want all the
annotations then people probably want to see all the phenotype matches from
human, mouse and fish but this could be hard to fit into a simple TSV with
one row per variant. It is definitely needed though. Been thinking an Excel
output which is similar to the HTML output would probably be popular.

On Fri, Jan 23, 2015 at 1:35 PM, Max [email protected] wrote:

You wrote in the exomiser draft protocol that there is a TAB delimited
file format. Right now there exists one for genes. I think if people using
pipelines it will be great to have a TSV-file with the variants and all the
annotations (still in the vcf-file annotations are missing).

I can start implementing this feature if it is OK with you.

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#28.

[visze]

But you cannot easily use Excel for parsing.

We have an actual case, where we want to use exomiser within a study. It should run automatically in a pipeline. After running exomiser, the results should be parsed back into the main database of the study. Right now, we have to parse the html output. That's horrible. the VCF-Infoline is not completed (transcripts, functional classes and so on are missing). The easiest way will be a tsv format.

I think the fundamental questionis: What is the motive for running Exomiser locally?
On my opinion there are two main reasons:

1. Run it locally, beacuse the user do not want to upload VCFs (privacy issue).
2. Run exomiser as part of a pipeline. So the variant results should be easily readably by a script.

[damiansm]

On Fri, Jan 23, 2015 at 3:06 PM, Max [email protected] wrote:

But you cannot easily use Excel for parsing.

I mean Excel as well as TSV of course. Excel for the clinicians - they have
asked for it.

We have an actual case, where we want to use exomiser within a study. It
should run automatically in a pipeline. After running exomiser, the results
should be parsed back into the main database of the study. Right now, we
have to parse the html output. That's horrible. the VCF-Infoline is not
completed (transcripts, functional classes and so on are missing). The
easiest way will be a tsv format.

Totally agree the TSV needs to include extra data. It was originally just
developed for me and my benchmarking! Can we get this done for the Nature
Protocols paper - ask Peter if timeframe is possible as I am away all next
week! I have been thinking for a long time this is needed.

I think the fundamental questionis: What is the motive for running
Exomiser locally?
On my opinion there are two main reasons:

1. Run it locally, beacuse the user do not want to upload VCFs
   (privacy issue).
2. Run exomiser as part of a pipeline. So the variant results should
   be easily readably by a script.

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#28 (comment).

[visze]

I also have a local version to annotate variants :-)

I have some time and can transfer it to the actual development version. The results will be look like (with some bugs):

#CHROM	POS	REF	ALT	QUAL	FILTER	GENOTYPE	COVERAGE	FUNCTIONAL_CLASS	HGVS	TRANSCRIPT	EXON	BASE_CHANGE	AA_CHANGE	EXOMISER_GENE	CADD(>0.483)	POLYPHEN(>0.956;>0.446)	MUTATIONTASTER(>0.94)	SIFT(<0.06)	DBSNP_ID	MAX_FREQUENCY	DBSNP_FREQUENCY	EVS_EA_FREQUENCY	EVS_AA_FREQUENCY	EXOMISER_VARIANT_SCORE	EXOMISER_GENE_PHENO_SCORE	EXOMISER_GENE_VARIANT_SCORE	EXOMISER_GENE_COMBINED_SCORE
chr10	123243197	G	A	65.25	Target	0/1	9	INTRONIC	FGFR2:uc001lfg.4:intron10:c.1125+15C>T	uc001lfg.4	intron10	c.1125+15C>T	0	FGFR2	0	0	0	0	0	0	0	0	0	0	1	1	0.9978677
chr10	123247670	C	-	692.49	Target	0/1	31	INTRONIC	FGFR2:uc001lfg.4:intron6:c.688-43G>-	uc001lfg.4	intron6	c.688-43G>-	0	FGFR2	0	0	0	0	0	0	0	0	0	0	1	1	0.9978677
chr10	123256215	T	G	100	PASS	0/1	0	MISSENSE	FGFR2:uc001lfg.4:exon6:c.518A>C:p.E173A	uc001lfg.4	exon6	c.518A>C	p.E173A	FGFR2	0.84209	0.998	1	0	rs121918506	0	0	0	0	1	1	1	0.9978677
chr9	94456643	G	C	166.26	Frequency	0/1	10	UTR3	ROR2:uc004ari.1:c.*1C>G	uc004ari.1	c.*1C>G	0	0	ROR2	0	0	0	0	rs923771	83.79	83.79	21.8797	18.3849	0	0.679293	0.81040007	0.7566463
chr9	94456705	T	A	72.48	Target	0/1	7	INTRONIC	ROR2:uc004ari.1:intron11:c.2066-12A>T	uc004ari.1	intron11	c.2066-12A>T	0	ROR2	0	0	0	0	0	0	0	0	0	0	0.679293	0.81040007	0.7566463
chr9	94485928	C	T	226.58	Frequency	0/1	16	UTR3	ROR2:uc004arj.2:c.*16G>A	uc004arj.2	c.*16G>A	0	0	ROR2	0	0	0	0	rs2230578	79.29	79.29	30.6305	22.946	0	0.679293	0.81040007	0.7566463
chr9	94486321	C	T	276.3	Frequency	0/1	36	MISSENSE	ROR2:uc004arj.2:exon9:c.2455G>A:p.V819I	uc004arj.2	exon9	c.2455G>A	p.V819I	ROR2	0	0	0	0	rs10761129	78.42	78.42	32.9805	23.9673	0	0.679293	0.81040007	0.7566463
chr9	94486381	G	A	429.46	PASS	0/1	40	MISSENSE	ROR2:uc004arj.2:exon9:c.2395C>T:p.P799S	uc004arj.2	exon9	c.2395C>T	p.P799S	ROR2	0.4968	0.996	1	0.33	rs141235720	0.3372	0	0.3372	0.0908	0.81040007	0.679293	0.81040007	0.7566463
chr9	94487066	C	T	298.58	Target	0/1	15	SYNONYMOUS	ROR2:uc004ari.1:exon9:c.1290G>A:p.=	uc004ari.1	exon9	c.1290G>A	p.=	ROR2	0	0	0	0	0	0	0	0	0	0	0.679293	0.81040007	0.7566463
chr9	94495608	T	C	348.79	Frequency	0/1	22	MISSENSE	ROR2:uc004ari.1:exon6:c.313A>G:p.T105A	uc004ari.1	exon6	c.313A>G	p.T105A	ROR2	0	0	0	0	rs10820900	62.58	62.58	35.4186	25.6695	0	0.679293	0.81040007	0.7566463
chr9	94519645	G	A	1573.06	Pathogenicity	0/1	112	UTR5	ROR2:uc004ari.1:c.-49C>T	uc004ari.1	c.-49C>T	0	0	ROR2	0	0	0	0	rs145568368	0.4651	0.1377	0.4651	0.1362	0	0.679293	0.81040007	0.7566463
chr17	17697094	CAG	-	398.05	PASS	0/1	33	NON_FS_DELETION	RAI1:uc002grm.3:exon3:c.870_872del:p.Q291del	uc002grm.3	exon3	c.870_872del	p.Q291del	RAI1	0	0	0	0	0	0	0	0	0	0.85	0.5879024	0.85	0.52203065
chr17	17697404	C	T	730.68	PASS	0/1	52	MISSENSE	RAI1:uc002grm.3:exon3:c.1142C>T:p.A381V	uc002grm.3	exon3	c.1142C>T	p.A381V	RAI1	0.54361	0.696	1	0.04	rs113208290	0.5051	0.5051	0.4651	0.1589	0.7757377	0.5879024	0.85	0.52203065
chr17	10532884	G	A	297.29	Target	0/1	21	INTRONIC	MYH3:uc002gmq.2:intron40:c.5796+30C>T	uc002gmq.2	intron40	c.5796+30C>T	0	MYH3	0	0	0	0	0	0	0	0	0	0	0.56803846	0.73	0.33966452
chr17	10533595	-	T	957.27	Target	0/1	53	INTRONIC	MYH3:uc002gmq.2:intron37:c.5457+10insA	uc002gmq.2	intron37	c.5457+10insA	0	MYH3	0	0	0	0	0	0	0	0	0	0	0.56803846	0.73	0.33966452
chr17	10535429	TTTTG	-	277.92	Target	1/1	6	INTRONIC	MYH3:uc002gmq.2:intron34:c.4957-96CAAAA>-	uc002gmq.2	intron34	c.4957-96CAAAA>-	0	MYH3	0	0	0	0	0	0	0	0	0	0	0.56803846	0.73	0.33966452

[damiansm]

Looks good to me. Make it so

sent from phone
On Jan 23, 2015 3:42 PM, "Max" [email protected] wrote:

I also have a local version to annotate variants :-)

I have some time and can transfer it to the actual development version.
The results will be look like (with some bugs):
#CHROM POS REF ALT QUAL FILTER GENOTYPE COVERAGE FUNCTIONAL_CLASS HGVS
TRANSCRIPT EXON BASE_CHANGE AA_CHANGE EXOMISER_GENE CADD(>0.483)
POLYPHEN(>0.956;>0.446) MUTATIONTASTER(>0.94) SIFT(<0.06) DBSNP_ID
MAX_FREQUENCY DBSNP_FREQUENCY EVS_EA_FREQUENCY EVS_AA_FREQUENCY
EXOMISER_VARIANT_SCORE EXOMISER_GENE_PHENO_SCORE
EXOMISER_GENE_VARIANT_SCORE EXOMISER_GENE_COMBINED_SCORE chr10 123243197
G A 65.25 Target 0/1 9 INTRONIC FGFR2:uc001lfg.4:intron10:c.1125+15C>T
uc001lfg.4 intron10 c.1125+15C>T 0 FGFR2 0 0 0 0 0 0 0 0 0 0 1 1 0.9978677
chr10 123247670 C - 692.49 Target 0/1 31 INTRONIC
FGFR2:uc001lfg.4:intron6:c.688-43G>- uc001lfg.4 intron6 c.688-43G>- 0
FGFR2 0 0 0 0 0 0 0 0 0 0 1 1 0.9978677 chr10 123256215 T G 100 PASS 0/1
0 MISSENSE FGFR2:uc001lfg.4:exon6:c.518A>C:p.E173A uc001lfg.4 exon6
c.518A>C p.E173A FGFR2 0.84209 0.998 1 0 rs121918506 0 0 0 0 1 1 1
0.9978677 chr9 94456643 G C 166.26 Frequency 0/1 10 UTR3
ROR2:uc004ari.1:c._1C>G uc004ari.1 c._1C>G 0 0 ROR2 0 0 0 0 rs923771 83.79
83.79 21.8797 18.3849 0 0.679293 0.81040007 0.7566463 chr9 94456705 T A
72.48 Target 0/1 7 INTRONIC ROR2:uc004ari.1:intron11:c.2066-12A>T
uc004ari.1 intron11 c.2066-12A>T 0 ROR2 0 0 0 0 0 0 0 0 0 0 0.679293
0.81040007 0.7566463 chr9 94485928 C T 226.58 Frequency 0/1 16 UTR3
ROR2:uc004arj.2:c._16G>A uc004arj.2 c._16G>A 0 0 ROR2 0 0 0 0 rs2230578
79.29 79.29 30.6305 22.946 0 0.679293 0.81040007 0.7566463 chr9 94486321
C T 276.3 Frequency 0/1 36 MISSENSE
ROR2:uc004arj.2:exon9:c.2455G>A:p.V819I uc004arj.2 exon9 c.2455G>A p.V819I
ROR2 0 0 0 0 rs10761129 78.42 78.42 32.9805 23.9673 0 0.679293 0.81040007
0.7566463 chr9 94486381 G A 429.46 PASS 0/1 40 MISSENSE
ROR2:uc004arj.2:exon9:c.2395C>T:p.P799S uc004arj.2 exon9 c.2395C>T p.P799S
ROR2 0.4968 0.996 1 0.33 rs141235720 0.3372 0 0.3372 0.0908 0.81040007
0.679293 0.81040007 0.7566463 chr9 94487066 C T 298.58 Target 0/1 15
SYNONYMOUS ROR2:uc004ari.1:exon9:c.1290G>A:p.= uc004ari.1 exon9 c.1290G>A
p.= ROR2 0 0 0 0 0 0 0 0 0 0 0.679293 0.81040007 0.7566463 chr9 94495608
T C 348.79 Frequency 0/1 22 MISSENSE
ROR2:uc004ari.1:exon6:c.313A>G:p.T105A uc004ari.1 exon6 c.313A>G p.T105A
ROR2 0 0 0 0 rs10820900 62.58 62.58 35.4186 25.6695 0 0.679293 0.81040007
0.7566463 chr9 94519645 G A 1573.06 Pathogenicity 0/1 112 UTR5
ROR2:uc004ari.1:c.-49C>T uc004ari.1 c.-49C>T 0 0 ROR2 0 0 0 0 rs145568368
0.4651 0.1377 0.4651 0.1362 0 0.679293 0.81040007 0.7566463 chr17
17697094 CAG - 398.05 PASS 0/1 33 NON_FS_DELETION
RAI1:uc002grm.3:exon3:c.870_872del:p.Q291del uc002grm.3 exon3 c.870_872del
p.Q291del RAI1 0 0 0 0 0 0 0 0 0 0.85 0.5879024 0.85 0.52203065 chr17
17697404 C T 730.68 PASS 0/1 52 MISSENSE
RAI1:uc002grm.3:exon3:c.1142C>T:p.A381V uc002grm.3 exon3 c.1142C>T p.A381V
RAI1 0.54361 0.696 1 0.04 rs113208290 0.5051 0.5051 0.4651 0.1589
0.7757377 0.5879024 0.85 0.52203065 chr17 10532884 G A 297.29 Target 0/1
21 INTRONIC MYH3:uc002gmq.2:intron40:c.5796+30C>T uc002gmq.2 intron40
c.5796+30C>T 0 MYH3 0 0 0 0 0 0 0 0 0 0 0.56803846 0.73 0.33966452 chr17
10533595 - T 957.27 Target 0/1 53 INTRONIC
MYH3:uc002gmq.2:intron37:c.5457+10insA uc002gmq.2 intron37 c.5457+10insA 0
MYH3 0 0 0 0 0 0 0 0 0 0 0.56803846 0.73 0.33966452 chr17 10535429 TTTTG

• 277.92 Target 1/1 6 INTRONIC MYH3:uc002gmq.2:intron34:c.4957-96CAAAA>-
  uc002gmq.2 intron34 c.4957-96CAAAA>- 0 MYH3 0 0 0 0 0 0 0 0 0 0 0.56803846
  0.73 0.33966452

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#28 (comment).

[julesjacobsen]

commit: 7029704
commit: 854a2fb
commit: f9ceac9