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Old 04-10-2012, 04:33 PM   #2
sdriscoll
I like code
 
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438
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try this. mpileup doesn't do too much. bcftools is the program that actually does the SNP calling.

Code:
samtools mpileup -uf ../genomes/Homo_sapiens/UCSC/hg18/Sequence/WholeGenomeFasta/genome.fa sorted.bam | bcftools view -bvcg - > sorted.bcf
bcftools view sorted.bcf > sorted.vcf
head sorted.vcf
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