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Old 09-27-2012, 11:51 PM   #2
Location: Zurich

Join Date: Mar 2010
Posts: 56

Hi krueml,

If you want to filter the bam file for a minimum mapping quality have a look at the -q option of samtools view:

samtools view -bq 20 your.bam > out.bam

If you want to see a "List of Phred-scaled genotype likelihoods" you should have a look at the output of your pipeline before using the awk command. The awk command also dismisses some header lines starting with '##' e.g.:
PHP Code:
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> 
Btw: Your link points to the description of samtools pileup, but you use mpileup. Afaik there are some differences between both for example mpileup does not provide a consensus...
dschika is offline   Reply With Quote