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Old 06-19-2012, 06:31 AM   #1
bnfoguy
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Exclamation Converting .sam to .vcf

I have some files in the .sam format which I obtained after I ran Stampy on some Cancer reads. I now have to convert the .sam files to .vcf files to do some analysis and am clueless on how to do the conversion. Any help or hints would be much appreciated.
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Old 06-19-2012, 06:46 AM   #2
Richard Finney
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Use samtools with mpileup and use bcftools command:
samtools and bcftools are part of the samtools collection.
PLEASE DO examine the options to each command and understand them.

samtools mpileup -R -d 1000 -l rangehg18.chr -uf hg18.fa test.bam | bcftools view -g - > test.vcf

additional note: you will want to convert your sam into a sorted bam ("test.bam" in the example above)

Last edited by Richard Finney; 06-19-2012 at 07:34 AM.
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