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##fileformat=VCFv4.1 |
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##samtoolsVersion=0.1.19-44428cd |
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##reference=file://ex1.fa |
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##contig=<ID=seq1,length=1575> |
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##contig=<ID=seq2,length=1584> |
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> |
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##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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##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> |
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##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> |
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##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> |
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##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> |
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> |
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##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads"> |
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed"> |
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##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> |
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##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> |
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##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint"> |
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##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio"> |
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##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio"> |
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##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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##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> |
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##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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##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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##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2."> |
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##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2."> |
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##INFO=<ID=QBD,Number=1,Type=Float,Description="Quality by Depth: QUAL/#reads"> |
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##INFO=<ID=RPB,Number=1,Type=Float,Description="Read Position Bias"> |
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##INFO=<ID=MDV,Number=1,Type=Integer,Description="Maximum number of high-quality nonRef reads in samples"> |
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##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken |
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."> |
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
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##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> |
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##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)"> |
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##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> |
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##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality non-reference bases"> |
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##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> |
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> |
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test.bam |
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seq1 993 . T A 61 . DP=136;VDB=5.035851e-03;RPB=2.097285e-01;AF1=0.5;AC1=1;DP4=44,29,35,27;MQ=60;FQ=63.5;PV4=0.73,1,1,1 |
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GT:PL:GQ 0/1:91,0,100:93 |
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seq2 303 . TC TCCC 103 . INDEL;IS=3,0.044118;DP=68;VDB=9.692566e-03;AF1=1;AC1=2;DP4=0,0,30,0;MQ=60;FQ=-125 GT:PL:GQ |
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1/1:144,90,0:99 |
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seq2 304 . C CCA 214 . INDEL;IS=52,0.800000;DP=65;VDB=4.882629e-04;AF1=1;AC1=2;DP4=0,0,46,0;MQ=60;FQ=-173 GT:PL:GQ |
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1/1:255,138,0:99 |
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seq2 837 . A C 68 . DP=128;VDB=2.587057e-02;RPB=3.599771e-01;AF1=0.5;AC1=1;DP4=41,25,30,32;MQ=60;FQ=67.5;PV4=0.15,1,1,1 |
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GT:PL:GQ 0/1:98,0,97:97 |
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seq2 893 . G C,A 143 . DP=110;VDB=4.352574e-03;RPB=-2.270745e+00;AF1=1;AC1=2;DP4=1,1,47,61;MQ=60;FQ=-282;PV4=1,1,1,1 GT:PL:GQ |
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1/1:176,255,0,178,255,175:99 |
That's really great, will save me a lot of disk space not to prepare yet another set of bam files.
EDIT . OK, I am scratching my head right now... so you only got only 5 additional SNPs having added an identical string to all the reads? But it seems to me you assigned low Phred quality values (2) to the added nucleotides, so SNP caller might be biased against them for that reason?