Hi Mathieu, for greater sensitivity, please try to increase the prior, it's the -P option in bcftools v1.0
Petr On Tue, 2014-08-26 at 16:15 -0400, Mathieu Bourgey wrote: > Hi all, > > I got a strange lack of call when I used samtolls mpileup + bcftools > to call my SNP (version 0.19 or 1.0 give me the same outputs) > > here as what I observe when I use samtools+bcftools view: > > samtools mpileup -q 1 -u -D -S -g -f hg1k_v37.fasta -r > 3:44775917-44775917 alignment/sample1.sorted.dup.recal.bam > alignment/sample2.sorted.dup.recal.bam > alignment/sample3.sorted.dup.recal.bam | bcftools view > > ##ALT=<ID=X,Description="Represents allele(s) other than observed."> > ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the > variant is an INDEL."> > ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of > reads supporting an indel"> > ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of > reads supporting an indel"> > ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> > ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias > for filtering splice-site artefacts in RNA-seq data (bigger is > better)",Version=3> > ##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of > Read Position Bias (bigger is better)"> > ##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of > Mapping Quality Bias (bigger is better)"> > ##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of > Base Quality Bias (bigger is better)"> > ##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test > of Mapping Quality vs Strand Bias (bigger is better)"> > ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based > metric."> > ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads > (smaller is better)"> > ##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used > for calling, see description of bcf_callret1_t in bam2bcf.h"> > ##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for > calling"> > ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of > Phred-scaled genotype likelihoods"> > ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of > high-quality bases"> > ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand > bias P-value"> > ##bcftools_viewVersion=1.0+htslib-1.0 > ##bcftools_viewCommand=view > #CHROM POS ID REF ALT QUAL FILTER INFO > FORMAT sample1 sample2 sample3 > 3 44775917 . A C,<X> 0 . > > DP=247;I16=207,1,36,0,6174,186100,1117,35331,12480,748800,2160,129600,3824,84932,643,14149;QS=2.65514,0.344865,0;VDB=0.986901;SGB=0.623532;RPB=0.19008;MQB=1;MQSB=1;BQB=2.58832e-10;MQ0F=0 > PL:DP:SP 0,90,152,90,152,152:30:0 20,0,115,255,185,236:112:0 > 0,42,110,255,149,215:102:0 > > when I then used: bcftools call -m -v I didn't get any variant called > whereas the PL field of the sample 2 (20,0,115,255,185,236) shows an > higher likelihood for the heterozygote call. > > Any idea what happens here ? > > thanks in advance > > Mathieu > > -- > Mathieu Bourgey, PhD > Chef d'équipe Production de Données et Services > Plateforme de bioinformatique > Centre d'innovation Génome Québec et université McGill > ------------------------------------------------------------------------------ > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
