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1 ##fileformat=VCFv4.1
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2 ##samtoolsVersion=0.1.18 (r982:295)
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
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5 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
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6 ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
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7 ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
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8 ##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
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9 ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
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10 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
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11 ##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
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12 ##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
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13 ##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
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14 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
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15 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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16 ##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
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17 ##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
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18 ##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
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19 ##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
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20 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
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21 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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22 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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23 ##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
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24 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
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25 ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
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26 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
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27 ##SnpEffVersion="3.4 (build 2013-11-27), by Pablo Cingolani"
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28 ##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -snp -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -stats /galaxy/PRODUCTION/database/files/000/376/dataset_376197.dat GRCh37.73 /galaxy/PRODUCTION/database/files/000/376/dataset_376194.dat "
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29 ##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 | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype_Number [ | ERRORS | WARNINGS ] )' ">
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30 ##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -geneId -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -stats /galaxy/PRODUCTION/database/files/000/376/dataset_376199.dat GRCh37.73 /galaxy/PRODUCTION/database/files/000/376/dataset_376196.dat "
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31 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /galaxy/PRODUCTION/database/tmp/tmp-SAMTOOLS-BmXdVn/bam_input_0.bam
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32 chr1 22846709 . G A 9.31 . DP=2;VDB=0.0174;AF1=1;AC1=2;DP4=0,0,1,1;MQ=20;FQ=-33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V885M|1127|ZBTB40|protein_coding|CODING|ENST00000374651|12|1) PL 40,6,0
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33 chr1 36752433 . C T 6.02 . DP=2;VDB=0.0099;AF1=1;AC1=2;DP4=0,0,2,0;MQ=20;FQ=-33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A201V|955|THRAP3|protein_coding|CODING|ENST00000354618|4|1) PL 36,6,0
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34 chr1 89449390 . T C 15.1 . DP=3;VDB=0.0214;AF1=1;AC1=2;DP4=0,0,1,2;MQ=20;FQ=-36;EFF=EXON(MODIFIER|||||RBMXL1|processed_transcript|CODING|ENST00000413769|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I40M|390|RBMXL1|protein_coding|CODING|ENST00000321792|2|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I40M|390|RBMXL1|protein_coding|CODING|ENST00000399794|3|1);EFF=EXON(MODIFIER|||||ENSG00000213516|processed_transcript|CODING|ENST00000413769|3|1) PL 47,9,0
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35 chr1 89449434 . T C 9.31 . DP=2;VDB=0.0120;AF1=1;AC1=2;DP4=0,0,1,1;MQ=20;FQ=-33;EFF=EXON(MODIFIER|||||RBMXL1|processed_transcript|CODING|ENST00000413769|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T26A|390|RBMXL1|protein_coding|CODING|ENST00000321792|2|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T26A|390|RBMXL1|protein_coding|CODING|ENST00000399794|3|1);EFF=EXON(MODIFIER|||||ENSG00000213516|processed_transcript|CODING|ENST00000413769|3|1) PL 40,6,0
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