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##SnpEffVersion="SnpEff 3.2 (build 2013-03-14), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -i vcf -o vcf GRCh37.66 /if2/arq5x/cphg-quinlan/projects/sms-elsea/varCalling/all.vcf "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon  | GenotypeNum [ | ERRORS | WARNINGS ] )' ">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	child_1	child_2	dad_2	mom_2	dad_1	mom_1	child_3	dad_3	mom_3	child_4	dad_4	mom_4
1	17363	.	TTCT	T	628.85	.	AC=2;AF=0.083;AN=24;BaseQRankSum=4.577;DP=2951;DS;FS=10.112;HRun=0;HaplotypeScore=316.7300;InbreedingCoeff=-0.0909;MQ=22.73;MQ0=27;MQRankSum=1.681;QD=1.33;ReadPosRankSum=0.329;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|8|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|5|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1)	GT:AD:DP:GQ:PL	0|0:250,0:70:99:0,169,3371	0|0:250,0:78:99:0,199,4105	0|0:250,0:70:99:0,187,3984	0|0:250,0:63:99:0,166,3406	0|0:243,0:89:99:0,262,5364	0|0:250,0:62:99:0,172,3575	0|1:205,27:73:99:371,0,3406	0|1:225,16:74:99:318,0,3528	0|0:250,0:64:99:0,193,3988	0|1:205,27:73:99:371,0,3406	0|1:225,16:74:99:318,0,3528	0|0:250,0:64:99:0,193,3988
1	17730	.	C	A	102.87	.	AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1)	GT:AD:DP:GQ:PL	0|0:246,4:250:36.11:0,36,464	0|0:244,5:249:57.17:0,57,727	0|0:244,6:250:48.15:0,48,628	0|0:247,3:250:51.13:0,51,621	0|1:242,8:250:26.26:26,0,830	0|0:246,4:250:48.14:0,48,601	1|0:221,13:234:13.85:14,0,482	0|1:232,11:243:7:7,0,501	0|1:238,12:250:73.18:73,0,368	1|0:221,13:234:13.85:14,0,482	0|1:232,11:243:7:7,0,501	0|1:238,12:250:73.18:73,0,368
1	17740	.	C	A	102.87	.	XX=;AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1)	GT:XX:AD:DP:GQ:PL	0/0:TTTT	0|0:.:244,5:249:57.17:0,57,727	0/0:.:244,6:250:48.15:0,48,628	0|0:.:247,3:250:51.13:0,51,621	0/1:.:242,8:250:26.26:26,0,830	0|0:.:246,4:250:48.14:0,48,601	1/0:.:221,13:234:13.85:14,0,482	0|1:.:232,11:243:7:7,0,501	0/1:.:238,12:250:73.18:73,0,368	1|0:.:221,13:234:13.85:14,0,482	0/1:.:232,11:243:7:7,0,501	0|1:.:238,12:250:73.18:73,0,368
1	17750	.	C	A	102.87	.	AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1)	GT:AD:DP:GQ:PL	0/0:246,4:250:36.11:0,36,464	0/0:244,5:249:57.17:0,57,727	0/0:244,6:250:48.15:0,48,628	0/0:247,3:250:51.13:0,51,621	0/1:242,8:250:26.26:26,0,830	0/0:246,4:250:48.14:0,48,601	1/0:221,13:234:13.85:14,0,482	0/1:232,11:243:7:7,0,501	0/1:238,12:250:73.18:73,0,368	1/0:221,13:234:13.85:14,0,482	0/1:232,11:243:7:7,0,501	0|1:238,12:250:73.18:73,0,368
1	17760	.	C	A	102.87	.	AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1)	GT:AD:DP:GQ:PL	0/0:246,4:250:36.11:0,36,464	0/0:244,5:249:57.17:0,57,727	0/0:244,6:250:48.15:0,48,628	0/0:247,3:250:51.13:0,51,621	0/1:242,8:250:26.26:26,0,830	0/0:246,4:250:48.14:0,48,601	1/0:221,13:234:13.85:14,0,482	0/1:232,11:243:7:7,0,501	0/1:238,12:250:73.18:73,0,368	1/0:221,13:234:13.85:14,0,482	0/1:232,11:243:7:7,0,501	0/1:238,12:250:73.18:73,0,368
2	17760	.	C	A	102.87	.	AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1)	GT:AD:DP:GQ:PL	0/0:246,4:250:36.11:0,36,464	0/0:244,5:249:57.17:0,57,727	0/0:244,6:250:48.15:0,48,628	0/0:247,3:250:51.13:0,51,621	0/1:242,8:250:26.26:26,0,830	0/0:246,4:250:48.14:0,48,601	1/0:221,13:234:13.85:14,0,482	0/1:232,11:243:7:7,0,501	0/1:238,12:250:73.18:73,0,368	1/0:221,13:234:13.85:14,0,482	0/1:232,11:243:7:7,0,501	0/1:238,12:250:73.18:73,0,368
