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
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