Hi there,
I'm struggling to request a kind of simple information from samtools.
I am using samtools on several bam files at the same time. I would like to get,
for each site of each sample, the number of reads carrying each of the
different alleles.
In my vcf file, I have the VP4 field (Number of forward and reverse ref and
alternative alleles used in variant calling reverse respectively) in the INFO
fixed field but this corresponds to the counts summed on all individuals. I
would like to get the same information but for each sample independently. Is
there a way to do that (besides running mpileup on each sample independently?)
Cheers,
Adrien
I am using the following 2 commands:
c=/cluster/project9/ All/*.bam
mpileup -uID -d 1000 -Q20 -f ref.fasta $c | bcftools view -bvcg -> snps.raw.bcf
&&
bcftools view snps.raw.bcf | bcftools/vcfutils.pl varFilter -d10 >
snps.flt_d10.vcf
------------------------------------------------------------------------------------------
Adrien RIEUX
Research Associate
UCL Genetics Institute
Faculty of Life Sciences
Department of Genetics, Evolution & Environment
Darwin building
LONDON WC1E 6BT
[email protected]<mailto:[email protected]>
http://adrienrieux.wordpress.com/
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