Hi, I'm using the new SAMtools and BCFtools versions (v1.0). Is there a manual for SAMtools v1.0 ? I can find one for BCFtools (http://www.htslib.org/doc/) but not for SAMtools and it looks like some commands changed (compared with the previous version).
Cheers, Adrien From: Rieux, Adrien Sent: 10 July 2014 10:40 To: '[email protected]' Subject: Alleles counts obtained for independent samples... 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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